Holy crap... Most of the games I would mention are NOT on this list! If anyone has ever even heard of some of these more obscure ones, please, let me know!
ATARI
Yar's Revenge (My favorite crappy game)
Defender
Pitfall
APPLE IIE
Odell Lake
Oregon Trail
Montezuma's Revenge
C64
Kid Niki: Radical Ninja (totally not the same game on Nintendo)
Roadwar 2000 (the best game of all time)
Alf
Ninja (not The Last Ninja... just NINJA)
Saboteur
The Human Race (also the best game ever)
The Bard's Tale series
Zork
NINTENDO
Ninja Gaiden (easily the best game ever)
Blaster Master (one of the best games of all time)
SMB 1, 2, and 3
Rush N' Attack
Ikari Warriors (actually, this is the arcade version of The Glory Road... the Nintendo version sucked balls)
Contra (up up down down left right left right B A B A start, FTW)
The Immortal (also easily the best game ever)
Castlevania 2: Simon's Revenge
Legend of Zelda 2: Link's whatever it was called
SEGA MASTER SYSTEM
Alexx Kidd, original
Golden Axe
Altered Beast
Rastan
SEGA GENESIS
Splatterhouse
The Haunting, starring Polterguy
The Phantasy Star series
SEGA CD
Lunar: The Silver Star
Lunar: Eternal Blue
Sewer Shark
Sol Feace
SUPER NINTENDO
Final Fantasy 3 (clearly, the best story and characters in a game, ever)
Chrono Trigger
Mario Paint (Oh, the movies I could make)
Super Street Fighter 2: The New Challengers
PC
As was mentioned, the old Apogee platformers
Where in Time is Carmen Sandiego
Star Trek 25th Anniversary, with the voices of the original cast
Castles
Battle Chess
I think anything past that ceases to be nostalgic...