I already posted this in the 3DSWare wishlist thread, but I just realized that it should be in the VC section. So I made a 3DS VC wishlist. Yay!
Anyway, I'll start this off:
I WANT GBA GAMES. Seriously, the lack of a GBA slot doesn't really help anyone who wants to play old games that are harder to find nowadays. Even the DS/DS Lite GBA slots couldn't play older GB/GBC games, so It's great that the VC will have GB/C games. But it would be awesome to have GBA games as well.

I want Drill Dozer and Pokemon

Link's Awakening

That's the only game I really care about seeing.

Since Turbo-Grafx16 games are coming to the eShop, I'm thinking it will later get Genesis/MD, Neo Geo, and Arcade Games. Either that, or we'll see those games remade as "3D Classics" since 3rd parties are allowed to use that (like Sega remaking their Genesis/MD & arcade games, SNK remaking Neo Geo games, etc.)

I also hope you can connect to other 3DSes with the VC games to play multiplayer games.

EDIT: I also hope Nintendo adds the color filtering option for original GB games if it doesn't have them at launch

GB/C

Mega Man V
Super Mario Land
Super Mario Land 2
Final Fantasy Legends
Final Fantasy Legends 2
Final Fantasy Legends 3
Final Fantasy Adventures
Kid Icarus: of Myths and Monsters
Both Blaster Master games (because I forget which ones were good)
Kid Dracula
Kirby in Dreamland
Kirby Dreamland 2
Duck Tales
Tetris
Donkey Kong Country
Dragon Warrior I & II
Dragon Warrior III
Dragon Warrior Monsters 2 both versions
Pokemon Gold
Crystalis
Wario Land 2
Wario Land 3
Warlocked
Shantae
Trip World
Mr. Gimmick
Wendy: Every Which Way
Asterix
Bionic Commando: Elite Forces
Ninja Gaiden Shadow
Monster Max
Nemesis 2
Hammerin' Harry
World Heroes 2 Jet
King of Fighters '96
Battle Arena Toshiden
Magical Chase
Quarth
Vattle Giuce
Solar Stricker
Trax
Aerostar
Battle Unit Zeoth
Burai Fighter Deluxe / Space Marauder
Toki Tori
Cat Trap
Chalvo 55
Gargoyle's Quest
Survival Kids
Ninja Boy 2
Rolan’s Curse
Rolan’s Curse II
Azure Dreams
Metal Walker
Cave Noire (japan only)
Dragon Heart
Great Greed
Knight Quest
Sword of Hope 1 & 2
Cannon Fodder
Kingdom Crusade
Another Bible
Revelations: The Demon Slayer

TurboGraphx:

Soldier Blade

Game Gear:

Aerial Assault
Aleste
Columns
Crystal Warrior
Defenders of Oasis
Dynamite Heady
Fantasy Zone Gear
Fatal Fury Special
GG Shinobi
GG Shinobi 2
Mega Man
Monster World 2
Ninja Gaiden
Panzer Dragoon Mini
Power Strike 2
Shining Force: Sword of Haija
Streets of Rage
Streets of Rage 2
Super Columns

oO Haven't Played! Oo

TMNT III: Radical Rescue!
Mega Man V
Wario Land 2
Donkey Kong
Kirby's Dreamland 2
Wario Land 3
Contra: Operation C
Kid Dracula

I'd just love to see all the pokemans on there (Gold, Silver, Crystal, Red, Yellow, Blue, (and maybe even green???)), oh and I want to see The legend of zelda Seasons and Ages, oh and this old power ranger game I used to play back in the day but never beat (nostalgia vaule )

Kid Icarus: Of Myths and Monsters (I really hope Nintendo doesn't pass this over just because it was never released in Japan)
Super Mario Land 2: Six Golden Coins
Donkey Kong Land series
Kirby's Dream Land 1 and 2
Tetris
Wario Land series
Mole Mania (Just to see what it's like)

Gameboy/Color:

Super Mario Land 2
Wario Land trilogy
Donkey Kong Land trilogy
Donkey Kong '94
Castlevania II: Belmont's Revenge
Kirby's Dreamland 2
Kid Icarus: Of Myths and Monsters

Game Gear:

Super Columns
Shining Force: The Sword of Hajya

Totally agree. I bought the game recently for a few bucks but it's a pain to play on my old GBA with totally worn out buttons where you have to press until your thumb hurts for it to register the command...

Radar Mission! Mode A is like the closest and most fun I'd ever played to Battleship on GameBoy. Can't really think of anything else at the moment I'd like to see except for the original Pokémon games. (I don't care if it was generally the same version as Blue, Green version is a must! Wii Virtual Console has imports, 3DS Virtual Console deserves em, too.) Also, it probably couldn't hurt to place some VirtualBoy titles, maybe 3D enhanced. I remember playing a little bit of WarioLand on it, never owned the system myself, though.

Links Awakening and The Oracle games.

Donkey Kong Land trilogy
Mega Man V
Shantae
Super Mario Land
The Legend of Zelda: Link's Awakening
The Legend of Zelda: Oracle of Ages/Seasons
Wario Land 3

I'm not that familiar with the GameBoy library so it is a rather small list. I will most likely purchase a few more games based on reviews.

1. Most important to me would be that they don't just cut multiplayer-modes but let you play them wirelessly.
2. A save mode like in the Wii's VC where you could just leave the game and the next time you start it exactly where you left off. I'd be more inclined to buy games without a save option or with long password codes on the 3DS VC then.
3. Make GBA games available.
4. Give me good games that are very expensive otherwise (like Shantae and GoldenSun for example).
5. reasonable prices

Playing any GB game on the GBA is a pain....It just doesn't feel right imo and the complete lack of a head phone jack is a total MISS. You can however pay a dongle-like adapter for your headphones that sticks out like a total sore thumb.lol
Not only that, the GBA shrinks down the screen a bit compared to how to it's slightly larger image on the GBC.

If only I had a GamePoy Light, OR if my GBC were modded with a back or front light. I just can't bare to play GB games on my GBA, and i can't stand playing GB games on my GBC because of the horrible dark screen....You seriously have to have a lamp hovering over your head and get in the perfect position to play it and to me that ISN'T fun...

Metal Gear Solid:Ghost Babel

Neo Geo pocket games especially Sonic Pocket Adv.

Don't know about GB/C but if/when GBA games come:

Every Pokémon game
Every Mario game
The Legend of Zelda: Minish Cap
Both Metroids
Kingdom Hearts: CoM
Advance Wars 1 & 2
Bomberman Tournament
Bookworm
Every FF game (especially FFTA)
Shining Force: Resurrection of the Dark Dragon
Wario Land 4
Both WarioWare games (Inc. and Twisted)

This is just a quick list, I'm sure there isn't everything I wanna

Duck Tales 1 and 2

My only wish is that the shop would open so that I can start giving Nintendo my money!