Handhelds / Portables
Game Boy - The Legend of Zelda: Link's Awakening
Game Gear - Super Columns (it's a GG exclusive, so it should count. But otherwise, Crystal Warriors.)
Virtual Boy - Virtual Boy Wario Land
Game Boy / GB Color (dual mode) - Hexcite (it's a board game conversion, but hadn't had a console release before I think... otherwise, Montezuma's Return.)
Game Boy Color (only) - The Legend of Zelda: Oracle of Ages
Neo Geo Pocket Color - The Last Blade (it's a remake, but feels different from the console games. Otherwise, Metal Slug: 2nd Mission.)
Game Boy Advance - Fire Emblem (7)
Nintendo DS - Picross 3D
PSP - Class of Heroes II (or for US releases, ie not counting previous Japan-only versions, Growlanser: Wayfarer of Time)
TV Consoles
Atari 2600 - Megamania (also on 5200, but the 2600 version came first)
Odyssey 2 - UFO!
Atari 7800 - Desert Falcon
NES - Super Mario Bros.
Sega Master System - Zaxxon 3-D
TurboGrafx-16 - Blazing Lazers
Genesis - Sonic the Hedgehog 3 & Knuckles
Turbo CD - Castlevania X: Rondo of Blood
SNES - Super Mario World
Sega CD - Lunar 2: Eternal Blue (the PS1/SAT remake isn't quite the same... but otherwise, SoulStar.)
Sega 32X - Shadow Squadron
Sega CD 32X - Fahrenheit
Saturn - Panzer Dragoon (the first one)
Playstation - Threads of Fate
Nintendo 64 - The Legend of Zelda: Ocarina of Time
Dreamcast - Skies of Arcadia
Playstation 2 - Gradius V
Gamecube - Eternal Darkness
Xbox - Panzer Dragoon Orta
Xbox 360 - The King of Fighters XIII
Wii - Super Mario Galaxy
I thought this second list would be an interesting one to put together as well. Top game for each system that has never been re-released on any other platform, including Virtual Console or other downloadable re-releases:
Handheld consoles
Game Boy - This should be Gradius: The Interstellar Assault, but I probably technically shouldn't count it because of the Europe-only colorized GB/GBC version in one of the Konami collections, so... Wave Race, maybe?
Game Gear - Super Columns (or otherwise, Royal Stone)
[Virtual Boy - still Virtual Boy Wario Land]
Game Boy / GB Color (dual mode) - Montezuma's Return (a classic remake, should this count? It does have new level maps and more features. Otherwise, probably the B&W version of Conker's Pocket Tales.)
Game Boy Color (only) - WarLocked
[Neo Geo Pocket Color - still The Last Blade]
Game Boy Advance - Summon Night: Swordcraft Story
[Nintendo DS - still Picross 3D]
PSP - similar to before, Growlanser: Wayfarer of Time, or if you don't count it because of the Japanese PS2 release, Class of Heroes.
TV consoles
Atari 2600: Buck Rogers: Planet of Zoom (yes, it's based on an arcade game, but it plays differently from any other version -- it's the only one that plays on a 2d plane.)
[Odyssey 2 - still UFO!]
[Atari 7800 - still Desert Falcon]
NES - TMNT III: The Manhattan Project
[Sega Master System - still Zaxxon 3-D]
TurboGrafx-16 - W-Ring: The Double Rings
Genesis - The Adventures of Batman & Robin (second: maybe Eliminate Down)
Turbo CD - Alzadick: Summer Carnival '92
SNES - Firepower 2000
Sega CD - If we don't count Lunar 2 because of the remakes, then SoulStar, unless you don't count that either because of the unfinished Jaguar CD and 32X prototype roms, in which case... Silpheed!
Sega 32X - Shadow Squadron
Sega CD 32X - N/A (all games are also on Sega CD)
Saturn - Panzer Dragoon II: Zwei
Playstation - Wipeout 3
Nintendo 64 - Wipeout 64 (followed by Goemon's Great Adventure, for those that don't want to count Wipeout 64 because most of the tracks are remixes of old ones)
Dreamcast - 4 Wheel Thunder
Playstation 2 - Final Fantasy XII
[Gamecube - still Eternal Darkness]
[Xbox - still Panzer Dragoon Orta]
Xbox 360 - Hydro Thunder Hurricane
[Wii - still Super Mario Galaxy]
