Hrm... I would say:

River City Ransom
Metroid
Kid Icarus

I'm kind of questioning whether I can really count the NES port of Wizardry I. But Metroid and Kid Icarus are similar enough I think I can slip it into my list.
Lessee... probably:

1) Double Dragon 1-3
2) Gunsmoke
3) Excitebike

I liked several others, too:

The Legend of Zelda
Cobra Triangle
RC Pro Am
Lunar Pool
Bump 'n' Jump
Tetris
Base Wars
Blades of Steel
Desert Commander
Contra
In response to Vortezz
Yeah it was pretty cool for its time, i just hated all the jumping lol i always feel a few screens now and then
In response to Geo
My favorite games for different systems are:

NES
1.Crystalis
2.Willow
3.Magic of Scheherazade

SNES
1.Chrono Trigger
2.EarthBound
3.Arcana

Sega
1.Shining in the Darkness
2.Phantasy Star 4
3.Super Hydlide(The only reason this game is on the list is because of the song Dragon!!...You really should listen to it.)

Gameboy
1.Sword of Hope
2.Ultima:Runes of Virtue
3.Zelda:Link's Awakening

Playstation 1
1.Final Fantasy 7
2.Chrono Cross
3.King's Field

N64
1.Quest 64
2.Zelda:Ocarina of Time
3.Doom 64
In response to Adam_ArchMage
NES (4 NES roms)
1. Final Fantasy I
2. Dragon Warrior IV
3. Metroid

SNES (uhh..last time i counted it was 17 roms)
1. Harvest Moon (damnit i cant stop playing it! its so fun!)
2. Final Fantasy III (Ff6j)
3. Final Fantasy Mystic Quest (LOOK! A MIDGET!!!)

PS1 (9 CDs)
1. Need For Speed:High Stakes
2. Megaman Legends
3. Spyro: Ripto's Rage

N64(dont have anymore ;_;)
1. Zelda: Ocarina of Time
2. F-Zero X
3. Star Wars Rogue Squadron

Sega(1 rom)
1. Sonic & Knuckles
2. Zero Wing (ALL YOUR BASE ARE BELONG TO US)
3.

Gameboy (10 roms)
1. Harvest moon 3 (DAMNIT ITS BETTER THAN HM FOR SNES!!!!)
2. Driver: You Are the Wheelman
3. Zelda: oracle of Seasons

GBA (1 rom)
1. Super Mario Advance
In response to The mothball
2. Driver: You Are the Wheelman

Driver on Gameboy?! Get yourself the Playstation version, or the PC version, dagnabbit!

...Actually, you'd probably be better off getting GTA3 for PC instead. At least GTA3 gives you a fighting chance of escape. If you have a PS2, though, then you'd be far better off getting the game for the console rather than the PC. PC ports of console games are normally quite graphically inferior (GTA3 isn't so bad, but it still has clipping and seam problems). =)
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