I'm no film geek but I know what I like (to adapt a cliché). I'd actually have trouble distinguishing what I consider masterpieces with what I consider my favourite films. Are the two mutually exclusive? For example Super Troopers is one of my favourites but I'd never consider it a masterpiece.

A few that I would put in both catagories:

One Flew Over the Cuckoos Nest
Godfather I and II
Once Upon a Time in America
Battle Royale
Dawn of the Dead
The Shining
The Shawshank Redemption