I think Boogie Nights is a pretty fantastic movie. Maybe it's not the most original thing stylistically, but it's probably one of the most entertaining movies of the 90s. And Alfred Molina is awesome in it.
Magnolia is like, 33% good, 33% zzzz, and 33% too indulgent.
Punch-Drunk Love is pretty good, but it's an off-kilter black comedy in a vein somewhat similar to Todd Solondz (except without the creepy sexual overtones), making it the sort of thing one would not watch frequently, and it's not the sort of thing most people would appreciate at all. Of all his movies, I think this one is the most interesting to talk about because it is so strange.