I think these movies should get their due. Each of them are excellent movies but underrated.
Ek Doctor Ki Maut (1990) - Pankaj Kapoor, Shabana Azmi, Irfan Khan, Deepa Sahi
Lamhe (1991) - Anil Kapoor, Sridevi, Anupam Kher
English, August (1994) - Rahul Bose, Tanvi Azmi, Mita Vashisht
Rockford (1999) - Nagesh Kukunoor, Nandita Das
Mr. and Mrs. Iyer (2002) - Rahul Bose, Konkona Sen Sharma
Matrubhoomi (2003) - Tulip Joshi, Sudhir Pandey, Sushant Singh, Aditya Srivastav
Hazaaron Khwaishein Aisi (2005) - Kay Kay Menon, Chitrangada Singh, Shiney Ahuja, Saurabh Shukla
Iqbal (2005) - Shreyas Talpade, Naseeruddin Shah, Girish Karnad
My Brother Nikhil (2005) - Sanjay Suri, Juhi Chawla, Victor Banerjee
Page 3 (2005) - Konkona Sen Sharma, Atul Kulkarni, Sandhya Mridul, Tara Sharma, Boman Irani, Bikram Saluja
Sehar (2005) - Arshad Warsi, Mahima Chaudhary, Sushant Singh, Pankaj Kapoor
Dor (2006) - Ayesha Takia, Gul Panag, Shreyas Talpade
Khosla Ka Ghosla (2006) - Anupam Kher, Boman Irani, Parvin Dabas
Gandhi, My Father (2007) - Darshan Jariwala, Akshaye Khanna, Bhumika Chawla, Shefali Shah
Johnny Gaddar (2007) - Dharmendra, Neil Mukesh, Rimi Sen, Vinay Pathak
Swami (2007) - Juhi Chawla, Manoj Bajpai
The Blue Umbrella (2007) - Shreya Sharma, Pankaj Kapur
And the list goes on.

There are so many more good movies which I haven't seen yet or couldn't recall.