There are quite many Talented yet Underrated Actresses in B'wood. But Some of the more prominent ones are:-
Konkana Sen Sharma
2. Tabu
3. Nandita Das
4. Tisca Chopra
5. Richa Chadda
6. Divya Dutta
7. Radhika Apte
8. Swara Bhaskar
9. Kirti Kulhari
10. Sayani Gupta
11. Kalki Koechlin
12. Shweta Tripathi
Edit:-
Tillotama Shome and Rasika Duggal for Qissa
Tanishtha Mukherjee
Surveen Chawla for Parched and Ugly
Edit 2:-
For those who're saying that 'These Actresses aren't Underrated because they've Won National Award'. This Argument is wrong! Just because they've Won National Award, doesn't means that they're Treated at par with other ‘Mainstream A Listed Actresses'. Underrated, here means that they don't get same attention from Media, Mainstream Award Shows and Big Production Houses. These Actresses usually don't get Same roles as Deepika Padukone or Kareena Kapoor.
Edit 3:-
Sorry for this late addition here but lately I remembered her, so thought to list her.
Nimrat Kaur (Honoury Mention)
Though some might think and start sayin that 'she's not underrrated' et cetera et cetera but I believe that she indeed is an Underrated Actress. After proving her Metal again and again, Even Hollywood gave her big projects and yet Our Nepotism filled industry (Bollywood) is still not Casting her in Women Centric and Strong Protagonist Roles.