Jeffrey Overstreet

1. (tie)  The Iron Giant / Toy Story 2
2. The Insider
3. The Dreamlife of Angels
4. Star Wars, Episode One: The Phantom Menace
5. Three Kings
6. Magnolia
7. Fight Club
8. The Sixth Sense
9. Eyes Wide Shut
10. Being John Malkovich
11. Princess Mononoke
12. Limbo

runners up The Limey, Cradle Will Rock
I would include "The General" and "The Celebration", but they're technically 
'98 films that were released here in '99.