There weren't many great movies in 1990's but here are my favourite 10:

(updated since I've seen great Giorgino)

1. Giorgino (Laurent Boutonnat, France, 1994)
2. Ridicule (Patrice Leconte, France, 1996)
3. Khrustalyov, My Car! (Aleksei German, Russia, 1998 ) 
4. Le Parfum d'Yvonne (Patrice Leconte, France, 1994)
5. Breaking the Waves (Lars von Trier, Denmark, 1996)
6. Maboroshi no hikari (Hirokazu Kore-eda, Japan, 1995)
7. Abraham Valley (Manoel de Oliveira, France/Portugal, 1993)
8. Seven (David Fincher, USA, 1995)
9. The Thin Red Line (Terrence Malick, USA, 1998 ) 
10.The Wind Will Carry Us (Abbas Kioristami, Iran, 1999)

Close contenders:
Three Colors: Red, Summer Tale, Groundhog Day, Mother and son, After life, Double Life of Veronique, Time of a Dancer