For me:
1. Khamoshi
2. Gangubai
3. Hum Dil De Chuke Sanam
Khamoshi of course, his first movie, has a heart-breaking sincerity and pathos, and terrific performances.
Gangu for the storytelling. Despite its length, the movie had all the ingredients to keep you hooked from start to finish.
HDDCS for the music, the way love was depicted and shown, and the poetry in the scenes. I didn't like the ending, though, but it did make me think. The movie was a work of art.
5