1) Super Nintendo
2) Arcade
3) Nintendo 64

Arcade
Amiga
Dreamcast

1) Sega Genesis
2) Sega Dreamcast
3) Super Nintendo

1) Commodore 64
Before I had any systems of my own, I played and coveted my friend's C64. To be able to play the games of my youth would be amazing. I cannot even count the hours I spent playing "In Search of the Most Amazing Thing", "Car Wars", "Impossible Mission" (which, for me, was impossible), and "Space Station Construction Kit". My favorite "simulation" game was on it in the form of "Echelon" from U.S. Gold. If GOG could get some of these games, it would be truly amazing.
2) Genesis
The first system that was "mine". I'd love to be able to play the Genesis Shadowrun game and the Shining Force Series.
3) NeoGeo
Samurai Shodown - 'nuff said.

1. SNES (Lot's of really good stuff here)
2. C64 (While these games really show their age, it still would be great addition for it's retro value.)
3. Amiga / Genesis (I know these two have some good games, but have never really used these platforms before so hard to say which)

Interesting...I was totally unaware of that. I think my "why pay for a game that you could legally download for free?" question still stands though. And I can hear some of you questioning the word 'legally', but I've been told (by a friend in law school right now) that, at least in Canada, most of the copyrights on these really old games won't hold water in court now.

1.Dreamcast
2.Arcrade
3.NeoGeo

Dreamcast
N64
Amiga

Update my wishlist:
1)Super Nintendo
Games:
Soul Blazer Trilogy, Donkey Kong Country 1&2, Prince of Persia(Original), Battletoads,all Squaresoft Games, Zelda: Link to the Past, Metroid Prime, Earth Bound,Metal Max Returns,Doom, Contra III, Pocky & Rocky
I am pretty sure they will be modable once on the PC.
2) Nintendo 64:
Games:
Zelda: OoC& Zelda: MM, Mario 64, Turok, all Rare games, James Bond,Super Smash Brothers,Mischief Makers
3) Sega Dreamcast:
Berserk
Shenmue....MOTHERFUCKING SHENMUE!

1. SNES
2. Dreamcast
3. N64

1: Dreamcast - some pretty good games on there, and as far as I know no one else is selling them.
2: Arcade
3: Nintendo 64

1. Amiga (by a clear mile for me.)
2. Sega Dreamcast
3. Nintendo 64
Mostly due to availability reasons, there's some games for Dreamcast and Nintendo 64 which I'd love to play again but are impossible to find. The same is true for Amiga but for hundreds of games.

Of those choices, I would probably be most interested in Amiga titles. I've always been curious about that platform, but I missed out on it completely back then. The Amiga was also an actual desktop computer, which I feel makes it a good fit for GOG's mission statement. I would also imagine that the games were typically developed with keyboard or simple joystick controls in mind, which means they should translate well to the PC (Amiga fans can correct me if I'm wrong).
Commodore 64 comes in second, for similar reasons.
SNES games are great and all - the SNES was my favorite console - but let's be honest, I wouldn't buy them. I've already played them to death. It isn't worth $5.99 to me to play A Link to the Past for the twelfth time.
I would not buy an N64 game from GOG, either. The N64 had a very strange controller, and I'm not going to try to map controls like that to either my keyboard or to my 360 pad. The N64 had a poor library overall, anyway.

1. NES
2.SNES
3 C64