N64
Sega Genesis
Super Nintendo

1. Sega Dreamcast
2. Sega Megadrive/Genesis
3. SNES
From both consumer and business perspectives, SEGA is my number 1 (and 2) option. They're quite PC-friendly these days and they're not afraid to whore out their classic games collection to all platforms. So I guess it would be easier for you to get distribution rights for their classic games. I put Dreamcast as my first preference because it gives you a more unique value compared to Megadrive/Genesis (which has been widely emulated).
And SNES in number 3 because IMHO it has the biggest AAA gaming catalogue among all other options.

1. Commodore 64
I never owned any of the other platforms, so that's my only vote.

Arcade
N64
C-64

1) Super Nintendo
2) Nintendo 64
3) Sega Dreamcast
I'd love to see any (quality, of course) games belonging to the above 3 systems on GoG.

C64
Amiga
SNES

Sega Dreamcast
Super Nintendo
Nintendo 64

1. Super Nintendo - I'd love some Street Fighter, Mario, Mega Man, Kirby, and Metroid!
2. Nintendo 64 - Gotta have Starfox and Zelda!
3. Sega Genesis - Sonic is a must!
All those games would go great with my Logitech Rumplepad 2 controller...

1. Super Nintendo
2. Sega Mega Drive / Genesis
3. Amiga
Frankly, I should have mentioned Super Nintendo only. No System ever offered better games, besides the PC of course. But the PC has some unfair advantages. ;)

1. Sega Dreamcast
2. Super Nintendo
3. Arcade

Super Nintendo - Still has some of the BEST games ever in my opinion. Simple as that.
Nintendo 64 - Emulation has always been so glitchy for me and Wii download section does not seem to have the greatest selection. Still some great games for the N64 though.
DreamCast - I picked this system up awhile back in what seemed to be opened, but mint condition (for a mere $8) and regret ever passing it up during it's time after buying a few games for it. Would love to try out some other titles for it.
Although in all honesty, I don't see people paying much for these games since I'm sure most if not all people who game just download them for free and play through emulation. Someone mentioned "Game Packs", this sounds nice, or just simply a lower price than $5 a pop for older systems. Either way I'm sure GOG would come up with something reasonable.

I really have no desire to play console games on my PC.
There are so many good old games for the PC that I would love to play again or discover for the first time. I thought the whole point with GOG.com was to make good old PC games available and playable on Win XP / Vista / 7 systems.
I think that it would be a bad thing if GOG suddenly started using their resources getting console games working on the PC instead of making PC games work on newer systems.
A NES game will always work in a NES console and either are not hard to get, but old PC games can be hard to get a hold of and almost impossible to get running on newer systems. That's why GOG is so important to me and the PC gamers around the world. You are not only making the games available, you are making them playable.
Most people own a Nintendo Wii and have through the "Virtual Console" shop already access to tons of old console games (even C64 games). The Xbox 360, PS3 and PSP have got a similar service, but none of them got any old PC games.
This also means that there's no chance in hell that Nintendo or Sony will allow their old games to be ported and emulated to run on the PC.
So please GOG, stick with PC games.
The PC gaming community really needs it.

Dreamcast
SNES
N64

1: The GameBoy Advance For all the CastleVania, Metroid, and Zelda games.
2: Super Nintendo Entertainment System
For A Link to the Past, and Super Metroid,
3: Nintendo Entertainment System
For The Legend of Zelda, the Adventure of Link, Metroid, Chrystalis, Faxanudu, Willow, the Goonies II and so-forth and so-on.
(What can I say? I like 2d Zelda, CaslteVania and Metroid games.)
(Other worthy mentions include the Nintendo 64 for Goldeneye and Ocarina of time, and of course, the PlayStation so that I could finally play CastleVania: Symphony of the Night.)