I can remember many such films.
Nayak the Hero (2001)
The Ek din ka CM was a well appreciated concept and the film wa technically well made. A remake of Shankar’s own film Mudhalvan, Nayak had everything to make it a hit but the film was a commercial failure because of Shankar's inability to control the budgets of his film. Anil Kapoor by no means could carry a film with a budget of 20 crores and the film despite earning 11 crores approx the film badly failed. But the film was a massive hit on Satellite television and has gained a cult following since then.
Andaz Apna Apna (1994)
Now considered one of the greatest comedy films of Indian cinema, Andaz Apna Apna failed because of delays (delayed by 3 years) and very poor marketing strategy and the influx of its casettes soon after its release which killed it's theatrical business. The making of this film was marred by so many disagreements and fights but the end result was quite soothing. The film gained a lot of appreciation and traction with time and is one of the most popular films of Indian cinema. With this Rajkumar Santoshi, known for intense movies like Ghayal, Damini, Ghatak proved his versatility.
Another great comedy film Hera Pheri (remake of Ramji Rao Speaking, a Malyalam film) also did average business in its original run but became a cult classic through television. Similarly Badhshah (1999) also failed at the box office but gained popularity through television. The reason of their theatrical business was quite the same. Hera Pheri starred two action heroes and one character actor and an art house film actress. Nobody expected them to deliver a comedy film of epic proportions. And Hera Pheri released alongside another comedy film Dulhan Ham Le Jayenge directed by David Dhawan who is known for comedy films. On the other hand, Hera Pheri was made by Priyadarshan who had made serious films like Gardish, Virasat, Muskurahat, Saat Rang ke Sapne etc. It took the audience some time to recognise the value of Hera Pheri and the business of the film grew with word of mouth.
With Badshah, Abbas Mastan and SRK were returning after years after Baazigar which was a revenge thriller drama. People were expecting something of that genre from Abbas Mastan who are known for suspense thrillers. Instead they delivered a hilarious albeit silly comedy copied generously from Hollywood movies.
Haasil (2003)
A film which established the career of Irrfan Khan was a commercial disaster earning merely 1.8 crores at the box office. But Irfan stole the show with his brilliant performance and was about supported by Ashutosh Rana and Jimmy Shergill. The film gained a lot of critical acclaim and got popularity over the years.
In the similar veins, we find films like Gulaal (2009) and Gangs of Wasseypur II (2012) which were also commercial failures but have gained massive cult following and lot of popularity on social media.