Can't do an "all-time best" list... but here are my 90's picks:
Last Exit to Brooklyn
State of Grace
Goodfellas
Miller's Crossing
The Krays
The Grifters
Rush
The Indian Runner
Rosencrantz and Guildenstern Are Dead
Slacker
Barton Fink
Night on Earth
Reservoir Dogs
Remains of the Day
Carlito's Way
Schindler's List
Killing Zoe
Quiz Show
Hoop Dreams
Crumb
Smoke
Kids
The Usual Suspects
Bottle Rocket
Fargo
I Shot Andy Warhol
Dead Man
Trainspotting
Basquiat
Trees Lounge
Swingers
Sling Blade
Cop Land
L.A. Confidential
The Ice Storm
U-Turn
Boogie Nights
Permanent Midnight
American History X
Rushmore
Hurlyburly
Office Space
Lock, Stock and Two Smoking Barrels
Meeting People is Easy
Election
Run Lola Run
Happy, Texas
Being John Malkovich
American Movie
Sweet and Lowdown
Magnolia
Boondock Saints, The
High Fidelity
American Psycho
Snatch
Memento