I'll assume the question is being asked for amateur films, i.e. films being made by people who haven't done any professional course in film making.
There have been two short movies made during my stay at IIT Bombay which I feel have been the best of the lot.
First one is, The Hungry Man. This one is a silent short film, and was made as an entry for Mood Indigo's short film making competition in 2008. It's a black & white film, and has a Charlie Chaplin kind of humor. The music is an original composition, which even now we rarely see in amateur college films.
Film Trivia: The makers of this film actually removed frames in between scenes so that actions don't look smooth and there is a little jerk in every action in the movie. This was done to make the film resemble more with the Charlie Chaplin films.
The second one is, Kindergarten Dreams. It was made in early 2010 and was probably the first* amateur stop motion animation film made by Indian college students.
* – I might be wrong about this fact, and if anyone knows otherwise, please feel free to comment and let me know about the other movie that was made before this one. But there is a good chance that I am correct about this one