Well here's my list. I'll try and add some commentary if possible, but of course some films haven't been seen in a long time. 

1990 
Ju Dou (China/Japan - Zhang Yimou) 
Twin Peaks: Pilot Episode (US - David Lynch) 
Mo' Better Blues (US - Spike Lee) 
Goodfellas (US - Martin Scorsese) 
Dances With Wolves (US - Kevin Costner) 
Ghost (US - Jerry Zucker) 
Bullet in the Head (Hong Kong - John Woo) 

1991 
Terminator 2: Judgment Day (US - James Cameron) 
Europa Europa (France/Germany/Poland - Agnieszka Holland) 
JFK (US - Oliver Stone) 
Raise the Red Lantern (China/Hong Kong/Taiwan - Zhang Yimou) 
Barton Fink (US - Joel and Ethan Coen) 
Silence of the Lambs (US - Jonathan Demme) 
The Fisher King (US - Terry Gilliam) 
Van Gogh (France - Maurice Pialat) 
A Brighter Summer Day (Taiwan - Edward Yang) 

1992 
Malcolm X (US - Spike Lee) 
Reservoir Dogs (US - Quintin Tarantino) 
Unforgiven (US - Clint Eastwood) 
Hard Boiled (Hong Kong - John Woo) 
Wayne's World (US - Penelope Spheeris) 
Rebels of the Neon God (Taiwan - Tsai Ming Liang) 
Dead Alive (New Zealand - Peter Jackson) 
Bram Stoker's Dracula (US - Francis Ford Copola) 
Bad Lieutenant (US - Abel Ferara) 

1993 
Dazed and Confused (US - Richard Linklater) 
Schindler's List (US - Steven Spielberg) 
Groundhog Day (US - Harold Ramis) 
Visions of Light: The Art of Cinematography (US/Japan - Stuart Samuels, Arnold Glassman, Todd McCarthy, Andrew Glassman) 
Carlito's Way (US - Brian De Palma) 

1994 
To Live (China - Zhang Yimou) 
Pulp Fiction (US - Quintin Tarantino) 
Baseball (US - Ken Burns) 
Natural Born Killers (US - Oliver Stone) 
Quiz Show (US - Robert Redford) 
Shawshank Redemption (US - Frank Darabont) 
Forrest Gump (US - Robert Zemeckis) 
Chungking Express (Hong Kong - Wong Kar Wai) 
Heavenly Creatures (New Zealand - Peter Jackson) 
Satantango (Germany/Hungary/Austria - Bela Tarr) 
71 Fragments of a Chronology of Chance (Austria/Germany - Michael Haneke) 
Through the Olive Trees (Iran - Abbas Kiarostami) 
Burnt by the Sun (France/Russia - Nikita Mikhaltov) 

1995 
Before Sunrise (US - Richard Linklater) 
Toy Story (US - John Lasseter) 
Ulysses Gaze (Greece/France/Italy - Theo Angelopoulos) 
Underground (France/Germany/Hungary - Emir Kustirica) 
Fallen Angels (Hong Kong - Wong Kar Wai) 
Casino (US - Martin Scorsese) 
The Beatles Anthology (UK - Bob Smeaton) 
Kids (US - Larry Clark) 
Clockers (US - Spike Lee) 

1996 
Fargo (US - Joel and Ethan Coen) 
Gabbeh (Iran - Mohsen Makhmalbaf) 
When We Were Kings (US - Leon Gast) 
Lone Star (US - John Sayles) 
The Celluloid Closet (US - Robert Epstein, Jeffrey Friedman) 
Forgotten Silver (New Zealand - Peter Jackson, Costa Botes) 
The Pillow Book (UK/France/Netherlands - Peter Greenaway) 
The Battle Over Citizen Kane (US - Michael Epstein, Thomas Lennon) 
Irma Vep (France - Olivier Assayas) 
Les Voleurs Thieves (France - Andre Techine) 

1997 
LA Confidential (US - Curtis Hansen) 
Boogie Nights (US - Paul Thomas Anderson) 
Titanic (US - James Cameron) 
Happy Together (Hong Kong - Wong Kar Wai) 
Deconstructing Harry (US - Woody Allen) 
Princess Mononoke (Japan - Hayao Miyazaki) 
Lost Highway (US/France - David Lynch) 

1998 
Saving Private Ryan (US - Steven Spielberg) 
Thin Red Line (US - Terence Malick) 
Rushmore (US - Wes Anderson) 
Flowers of Shanghai (Japan/Taiwan - Hou Hsaio-Hsien) 
John Leguizamo's Freak (US - Spike Lee) 
After Life (Japan - Hirokazu Kore-eda) 
Run Lola Run (Germany - Tom Tykwer) 
The Mirror (Iran - Jafar Panahi) 

1999 
Magnolia (US - Paul Thomas Anderson) 
Fight Club (US - David Fincher) 
Toy Story 2 (US - John Lasseter, Lee Unkrich, Ash Brannon) 
South Park: Bigger, Longer, and Uncut (US - Trey Parker) 
American Beauty (US - Sam Mendes) 
Three Kings (US - David O'Russell) 
Election (US - Alexander Payne) 
The Emperor and the Assassin (China/Japan/France - Chen Kaige) 
The Matrix (US - Andy and Larry Wachowski) 
Bringing Out the Dead (US - Martin Scorsese) 
The Hurricane (US - Norman Jewison) 
The Iron Giant (US - Brad Bird) 

*Edit for Burnt by the Sun and Through the Olive Trees