What are the uniqueness of various Indian temples?

 I shall mention a few that I have personally been to and I have been told/witnessed these myself.

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Chidambaram Thillai Nataraja Temple, Chidambaram, Tamil Nadu

The temple is run by the Pothu Deekshitars who are believed to have been brought down from Mount Kailas by Lord Nataraja Himself. They are the traditional owners and trustees of the temple. The temple and its premises were forcibly taken over by greedy politicians and bureaucrats to feed off their revenue. In a landmark judgment in 2014, the Supreme Court asked the state to return the temple back to the rightful owners (SC frees Nataraja temple from TN Govt's control)

Only married men are allowed to touch the idol and do the daily poojas.

Only men who have hair on their heads and are able to grow it into a length long enough to tie it into a kudumi (bun) are allowed to be priests. (Tamil Nadu's Dikshitars on the verge of extinction)

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Thirunelli Maha Vishnu Temple, Wayanad, Kerala

Before there were motors, people had to carry and bring up pots of water up to the top of the hill where this temple is situated for conducting the daily rituals. Once a local elite lady saw the suffering of the people and commissioned a granite/stone waterway to be built from a stream downhill from where the people used to collect water all the way up to the temple. The waterway still stands even to this day. Not an ounce of mortar or any binding agent has been used to bind the stones together. the rocks just fit together and water flows UPHILL. Even now, it is is this water that is used for daily poojas in the temple. I have actually gone and stood under the waterway to see if any leakage is there. Nope. Nothing.

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Kashi Vishwanath Temple, Varanasi, Uttar Pradesh

In the entire city of Kashi, it is said that no flowers will emit any fragrance. Dogs will not bark. And lizards will not chitter. Kashi is said to be a cremation ground.

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Anegudde Sri Vinayaka Temple, Kumbhashi, Udupi, Karnataka

The idol in this temple grows in size. Lord Vinayaka of Anegudde wears a silver armor/ breastplate which has to be changed frequently because it would break at the sides after a while due to the idol growing in size.

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Sree Poornathrayeesa Temple, Tripunithura, Kerala

This is probably the only temple where the idol of Lord Ganesha faces the South direction. As per temple legends, the idol of Lord Poornathryeesha was brought down from Vaikuntham by the Pandava prince Arjuna and Lord Krishna to commemorate their visit to bring back the Brahmin’s children (a story in the Mahabharata). It was Arjuna who was carrying the idol and he requested Lord Ganesha to go ahead of him and find a good place to consecrate the idol. Lord Ganesha found a spot in Poornavedapuri on the banks of the Poorna river to be the most auspicious spot. Poornavedapuri got its name as it was one of the main centers of Vedic teaching in the region. Lord Ganesha found the spot to be so auspicious that He occupied the spot Himself. When Arjuna arrived at the scene carrying the idol in his hands, he saw Lord Ganesha seated comfortably at the ordained spot. Arjuna requested Lord Ganesha to move, but He would not budge. Arjuna could not keep the idol down anywhere else as it would be fixed to that spot thereafter. After repeated requests, Lord Ganesha refused to move an inch. The idol was growing heavier in his arms and Arjuna could bear it no longer. It is said that he gave a shove to Lord Ganesha with his foot to the left side and placed the idol of Lord Vishnu at the same spot.

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Chottanikkara Bhagavathi Temple, Chottanikkara, Kerala

This temple is the ultimate testimony of the importance of Shaktya tradition of worship and of the importance of Tantric practices being followed in Kerala. The deity here is that of the female goddess who is worshipped as Goddess Saraswati in the morning, as Goddess Lakshmi at noon and as Goddess Parvati/Shakti in the evening.

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Mannarasala Sree Nagaraja Temple, Alappuzha, Kerala

The priest here is the oldest female member of the Namboothiri family which is the traditional owners of the temple as she is said to symbolize the mother of Lord Nagaraja, the main deity there. Only she is allowed to do the main pujas in the temple.

After her death, the next oldest female member assumes the position.

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Sree Pattabhirama Temple, Tripunithura, Kerala

The temple is owned and run by the Goud Saraswat Brahmin community. It is prohibited for anybody from any other caste to enter the main shrine of Lord Pattabhirama. A lot of people, however, visit the temple and stand outside the main shrine to pray. The small shrine of Lord Hanuman located to the left of the main entrance also draws a lot of devotees every day.

Why are idols in South Indian temples kept in dark with no lights?

The Statues-Idols are kept in Karpa-Graha of the Temple.

• The term "karpa graha" refers to the sanctum sanctorum of a Hindu temple, also known by the Sanskrit term garbhagriha . In Tamil, it is called karuvarai, which means "womb chamber," derived from the words "karu" (foetus) and "arai" (room).
• I’m not sure what is reality behind the closure of Karpa-Graha without any light nor celebrating the Statues-Idols in Karpa-Graha using Lamps-Lights-Sounds on specific days of the year.
• There should be wider meaning for the timely celebration and closure of temples on-time and every-time.
• Exception: Few temples are just opened for once in year or once in 14 years, many temples are opened daily.
• For Instance, Sabarimala Temple do manage a specific calendar for the opening and closure of Temple.

What are some mysterious scientific facts about Indian temples?

 When people speak about INDIAN TEMPLES, Temples of Tamil Nadu form an important part.

Tamil Nadu known as Land of Temples is a home to many ancient and beautiful temples.

If you enter by any way into TN, there will always be a temple to welcome you.

Each village/city/town is built around a TEMPLE in Tamil Nadu and TN has no less number of facts and mysteries.

Some of the mysterious cum scientific facts of such Temples are listed below.( the answer is little big)

1.Madurai Meenakshi Amman Temple

This famous temple of TN was nominated for the 7 wonders of the world with 33000 sculptures in this Temple,its built in the angle of 23 and a half degrees coinciding with the axis of earth that means all temples are built without an angle with respect to rising and setting but this temple is built very straight to north and south

Its still unknown how come the ancient kings built it so perfectly .

one more mysterious fact is that no fishes live in the golden lotus pond of this Temple though the Goddess here is known as MEENAKSHI OR GODDESS WHO HAS EYES THAT OF FISHES, still how much ever you leave a fish inside this pond, it dies off soon.

One more fact is this temple has the highest number of 14 Gopurams and no other temple in India as such number of very high and 14 Gopurams .

2.Thiruvannamalai Arunachaleshwarar Temple.

This beautiful ancient 25 acre Temple for Lord Shiva has a story that is as old as creation of universe.

Normally Tamil Nadu follows Agama Shastras ( a combination of the Vedic Hinduism and Dravidian Hinduism) and in Agama temples, there is a concept of Veedhi Ula( procession) wherein GOD made of Pancha Loham is taken outside once in a year or for a period of 10 days in a year and that time the god is taken out only by the main entrance way.

But in this temple, the GOD comes out by the adjacent way next to MAIN GOPURAM and its the only temple that follows this way and the reason is unknown.

3. Thirukovillur Vishnu Temple

Normally in all the temples of India, Lord Vishnu have his CONCH OR SHANGU in his left hand and Chakra in his right hand but this temple is special.

Here Vishnu have his conch in right hand and chakra in his left hand with his right feet raised above.

4.Chidambaram Natarajar Temple.

In India, every God has his own temple and even if two main gods have a temple, you should worship them in different sanctoms but in Chidambaram Temple, you can worship GOVINDARAJA PERUMAL and LORD NATARAJA by standing at one point which is very rare and you can’t witness such type of Darshan in any other temple of world.

In all the temples, only the Uthsava Murthy comes out for procession but in this temple Moolavar or the main God(the God inside the sanctorium) comes on Veedhi ula( procession).

This is the ONLY TEMPLE in India which celebrates both Thiruvadhirai festival for Lord Shiva( day on which universe was created) and Vaikunta ekadashi for Vishnu ( day on which the doors of Vaikuntam opens where according to beleif whoever dies on this day can get an oppurtunity of going to heaven irrespective of his karmas)

5.Thirunageshwaram Uppiliappan Temple

This temple in Kumbakonam,known as the temple town of Tamil Nadu, is very special temple for Hindus.

The reason is due to the Prasadam given in this temple.

Actually till now salt has never been added into any of the PRASADAMS done in this temple but still after pooja is done, the naivedhyam offered to GOD tastes very good as if salt is added in it but the makers don’t add even a pinch of salt into it.

6.Rameshwaram Ramanathaswamy Temple

In the Shiva Temples of Tamil Nadu , the poojari gives Vibhoothi and in Vishnu Temples the poojari gives Theertham but in Rameshwaram ,this way is opposite.

The shiva Temples of Ramehwaram give Theertham of Lord Vishnu and Vishnu Temples give Vibhoothi of Lord Shiva.

7.Alwarpalli Natarajar Temple

The murthy of ALWAR NATARAJAR TEMPLE is of a special one because Natarajar murthis are always made of PANCHALOHA ( a combination of 5 metals) but the murthy of this temple is made of stone and this stone is very special as it gives the sound of bronze metal when striked lightly.

8.Ratnagiri Murugan Temple,Vellore

A miraculous thing happens everyday in this Temple.

Milk turns into curd after Abhishekam.

Yes, you heard it right.

You yourself can witness this event of milk turning into curd after the Abhishekam in done.

9.Kulithirai Manaparai Temple ( Ratnagiri Malai)

This temple is present on an hillock .

The mysterious thing that happens on this hill is absence of birds flying over it.

Though you can find birds flying near this hill to the surface, its unknown why none of those birds neither fly nor sit on the branches of trees on this hill but you can climb and visit the Temple.

10.Keralapuram Temple, Kanyakumari

Though this temple is for Lord Shiva, the Ganapathi present under the Banyan tree of this Temple is very famous for his color changing phenomenon.

During the Uttarayana Kaala, the colour of the Vigraham remains WHITE while in Dakshayana Kaalam, the colour of Ganapathi Vigraham turns black.

The reason that they say is that the vigraham is made up of CHANDIRA GAANDA KAL (a type of stone that changes color according to seasons and suns rays).

12.Samayapuram Mariamman temple

One of the famous Devi or Amman temples of TN, the vigraham of this temple is very big and is not made up of stone.

The vigraham is made up of medicinal plants just like the PALANI MURUGAN TEMPLE that is made up of NAVAPAASHANAM( where the murthy is made up of mixing 9 poisonous plants) but still the you can drink the milk poured on these Vigrahams.

13. Surli malai, Theni

Surli is a place in TN that is famous for its caves and in one such caves you can find a Shivalingam and a Nandi.

The mud surrounding this cave is just like Vibhoothi or sacred ash of LORD SHIVA and it gets continously accumulated.

14.Senji malai Murugan Temple

Normally curds are always sour in taste but the curd that is poured on the vigraham of this Lord Murugan Temple doesn’t taste sour but it tastes sweet after Abhishekam.

Note:- I know that Some of the facts you can't understand while reading my answer but those who knows Agamas can clearly understand regarding Uthsava Murthy and all as this facts are regarding Agama Temples and worship.

There are more such unique facts about the Temples of Tamil Nadu.

What are the mysteries that you found in temples in India?

 Below are a few of many mysteries of Indian temples.

1. Musical staircase of Airavateswara temple

This temple is one of the greatest mysteries known to the mankind.

This lord Shiva temple was built by Raja Raja Chola 2 in 12th century CE. It is located near Kumbakonam in TamilNadu state, India. It is recognized as world heritage site by UNESCO. The entrance of temple which is made of stones produces 7 different sound notes when stepped at different points.

2. Lepakshi temple. Hanging pillar.

The Lepakshi temple is located in Andhra Pradesh. This temple has a total of 70 pillars and is known for its architectural beauty. But what catches hold of ones interest is that 1 pillar hangs in the air without any support. People often test it's reality by passing a cloth piece from below the pillar.

3. The Granite temple.

The Brihadeswara temple located in Tanjavur of TamilNadu state is well known for it's beautifully carved structure of Granite. But what catches hold is that there in no source of granite within 60km range of the temple.

The Gopuram of the temple weighs 80 tons. The mystery still exists of how such a heavy Gopuram was placed at top of the temple without any modern machinery.

4. Anantha Padmanabha swami temple

This temple is located in Tiruvananthapuram, India. It has 7 secret vaults. On the request of the Supreme court, the temple authorities opened the first 6 vaults unveiling a total wealth of 22 Billion dollars. The seventh vault is made of steel and doesn't has any latch. There are 2 cobras carved on the door. It is believed that this vault can only be opened by a secret chant. If any other means are used to open it then it may bring apocalypse. This temple remains the biggest mystery.

5. Flag waving in the opposite direction of the wind flow

The famous Jagannath temple located in Puri is a very important pilgrimage as it is one of the char dham. There is a flag on top of the temple. But the flag waves in the opposite direction of the wind flow. No one knows why.

Everyday a priest climbs the top of the temple which is as high as a 45storey building and changes the flag. If by any chance the flag isn't changed for even a day then the temple must remain closed for 18 yrs.

6. Nandi idol ejecting water with unknown source

The Kadu Malleshwara temple in Bangalore, karnataka is a temple dedicated to lord shiva. In 1997 some construction workers found a buried temple of nandi. The nandi idol does ejects water from it's mouth, the source of which is unknown till date. The water is very clean and flows to the Shiva Linga.

7. Rain predicting temple

The Jagannath temple in kanpur is also known as Rain Predicting temple. The top of the temple drips water droplets which are helpful in rain prediction. If the size of the droplet is small then it means draught and if it is bigger then it means a good rainfall. It predicts the monsoon well before the monsoon season(15 days before). Hence, the farmers in the nearby areas harvest their crops accordingly. The temple was constructed a few hundred yrs ago.

Edit 1:- Adding a few more as suggested by @Nandini Krishnan ma'am in comments.

8. The disappearing temple of Gujarat.

At the bay of Cambay on the beaches of Jambusar city there lies a 150yr old temple of Stambheshwar Mahadev. The speciality of the temple is that when high tide arrives, the temple completely submerges underwater and disappear from the sight. It re-emerges once the tide is passed.

9. Nidhi Van- where Lord Krishna visits himself

This temple is counted among the most mysterious temples of India. Nidhivan is a forest with the holy temple-Rang Mahal located in the temple city of India- Vrindavan. The temple is dedicated to Lord Krishna. Apart from holding several mythological beliefs, the activities that take place in and around the temple are beyond explanation. Nidhivan is a dense forest with the lush green trees. The interesting thing is that the barks of the trees are hollow and the land is absolutely dry, but the tree remains loaded with green leaves throughout the year. No tree stands straight and is bend towards the earth. Devotees believe that trees perform Rasleela at the night. Coming to Rang Mahal, there is a deity of Lord Krishna decorated beautifully. The temple is shut after the evening prayer and various things such as saree, sweets, betel nuts are kept inside the temple. Every morning the priests see that sweets are partially eaten and the clothes have been used. No one is allowed on the premises of the temple after the sun sets down. It is believed that Radha-Krishna comes to the temple every night to rest. Anyone who has tried to see what happens in the night either dies, go blind or become insane. The place remains mysterious till date.

10. The temple of eternal flames

Jwala ji temple is located in the Kangra district of Himachal Pradesh. Temple is dedicated to Sati, wife of Lord Shiva. What may leave you in dismay here is the eternal flame that is burning in the premises of the temple for 100 years without any source of fuel. If the mythological story is to be believed then Sati killed herself after her father mistreated Shiva. After her death, Lord Vishnu divided her body into 51 pieces which fell on different parts of Earth. The tongue is believed to be fallen at this place where Jwala Ji temple has been constructed. Many scientific organizations have come here to research about the source of this eternal flame but have failed.

11. The Linearity of Chidambaram Nataraja Temple, Kanchipuram Ekambareshwar temple, and Sri Kalahasthi temple.

Some mysterious temples have left people in awe. In the era where there were no scientific tools, three temples were built in the exact same longitudes at 79 degrees 42 minute east. The Chidambaram Nataraja temple in Tamil Nadu, Kanchipuram Ekambareshwar temple in Kanchipuram district of Tamil Nadu and Sri Kalahasthi temple in Andra Pradesh all lies on the straight line. These temples are considered to be Shiva lingam representing various elements of earth. Such as air, earth and space. The fact that it was built thousands of years ago where there were no scientific tools to measure the point on earth leaves many people in dismay. Some consider it to be a co- incidence. But, even if it is a co-incidence it is worth noticing.

12. Sugali Mata temple, the story of titled necks of deities

Located in the Auwa, Marwar district of Rajasthan. This temple has another mysterious story to unfold. The deities inside the temple have a tilted neck and remains tilted no matter if you try to change the idol or reconstruct it. People have tried several times to change the deity with a perfect one, but even the perfect idol tilts its neck after some time. And, those who try to change the deity falls sick. Many believe the reason behind the tilted neck is that, many freedom fighters used to visit this temple. Once, this deity was shot by a Britisher giving it a reason to have tilted neck.