http://en.wikipedia.org/wiki/Category:1999_video_games

My top 10 wasn't that hard this year.

1. Super Smash Brothers
2. Legend of Dragoon
3. Ape Escape
4. Valkyrie Profile
5. Final Fantasy VIII
6. Harvest Moon: Back to Nature
7. Parasite Eve II
8. Pokemon Gold/Silver
9. Um Jammer Lammy
10. Age of Empires II: Age of Kings
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11. Resident Evil 3 Nemesis
12. Power Stone
13. Pokemon Snap!
14. Space Channel 5
15. Silent Bomber
16. Pokemon Stadium
17. Mario Party 2
18. Pacman World
19. Strider 2
20. Syphon Filter
21. The Typing of the Dead
22. Dance Dance Revolution 3rd Mix
23. Dead or Alive 2
24. SNK vs. Capcom
25. Rayman 2: The Great Escape

1. Legend of Dragoon
2. Final Fantasy VIII
3. Final Fantasy Anthologies
4. Parasite Eve II
5. Wild Arms 2
6. Resident Evil 3 Nemesis
7. Dino Crisis
8. Valkyrie Profile
9. Chrono Cross
10. Unreal Tournament
11. Silent Hill
12. Strider 2
13. Tony Hawk Pro Skater
14. SNK vs. Capcom
15. Alundra 2: A New Legend Begins
16. Hydro Thunder
17. Earthworm Jim 3D
18. Croc 2
19. Super Smash Brothers
20. Worms Armageddon

Absolute Fave
Final Fantasy VIII

Liked Games
Crazy Taxi (but, the GameCube release from a couple years later)
Hybrid Heaven
Hydro Thunder
Legend of Dracoon
Lode Runner 3-D
Ogre Battle 64
Pokémon Gold and Silver
Pokémon Pinball
Pokémon Snap
Pokemon Stadium
RollerCoaster Tycoon
Star Wars: Episode 1: Racer: An extra colon for good measure
Super Smash Bros
Tai'Fu: Wrath of the Tiger

Rather Disliked Games
Donkey Kong 64
Final Fantasy Anthology
Jet Force Gemini

Absolute Bafflement
Chrono Cross. I want to like this game. I really do. But the battle system puts me to sleep.

I agree with you on the Chrono Cross bit. I too want to love the game too... specifically since I consider Chrono Trigger the absolute game ever. Besides the boring battle, the majority (if not all) of the 45 (or was it 54?) character were about as interesting as a brick. I'd much prefer CT's 7 well developed characters than the 40 plus garbage characters from CC. Yet another example of quality over quantity.

Arc the Lad Collection
Darkstone
Evolution
Final Fantasy Anthology
Harvest Moon Back to Nature
King of Fighters '99
Legend of Dragoon
Monster Rancher Battle Card Game
Mr. Driller
SaGa Frontier 2
Saiyuki: Journey West
Star Ocean: The Second Story
Threads of Fate
Tomba!2
Torneko: The Last Hope
Valkyrie Profile
Wild Arms 2

I never noticed til now just how spoiled I was. I loved all these games. This is actually a trimmed list too.