1) Dreamcast
2) Super Nintendo
3) Nintendo 64
Dreamcast, because it is pretty difficult to find the hardware/games used at this point. There are several Dreamcast-exclusives that I've wanted to try for a while.
SNES, because it has a freaking incredible library of games. Especially the classic platformers are great.
Nintendo 64, for the same reasons as the Dreamcast, but to a lesser extent.
Also, Steam recently started selling old Genesis games... not sure if you want to compete that directly or not, but you guys should know anyway. In case you didn't already.

1. Amiga (i'd love to replay that Blues Brothers game...)
2. Neogeo (SSF2...)
3. Sega Megadrive (Golden Axe...)

1. Dreamcast (didn't hear about till they discontinued it)- because some of the games looked interesting
2. N64, this is where i played some of Favourite Console Games, so this potentiality would be great too. (Could be awesome to Have a GoG Edition USB N64 Controller)
3. Mega Drive

1) Amiga
2) Commodore 64
3) Super Nintendo

1 - Dreamcast (a lot of interesting games)
2 - NeoGeo (games hard to find now, as far as I know)
3 - N64 (some great games)
But well, actually, if there was something like that, for me it would be really less interesting than all the computer games we can find out here.

Missing some Platforms on that list:
Sega Saturn/Master System/Game Gear
Game Boy/Color/Advance
Atari Computers/jaguar/Lynx/2600
3DO
Philips CDi (although... no very GOOD old games on this one ;) )
But it's already a great choice!
1. dreamcast
Some of the best games I ever played but can't find them anymore around
2. Amiga
Had also some very good games
3. Arcade
For some games the only good version was the arcade version. Even if some will be surely lame without the right cabinet

1. SNES
2. Amiga
I don't know what most of the other choices are like aside from the N64 which i own.

1) Dreamcast
2) N64
3) SNES
But I agree this might not be the best move for GOG. If you know enough to want these old games your probably either emulating or own the hardware still already and although its really not how it should be, lets just say theres a number of methods already (most of which I'm not condoning) that make playing games of this age fairly cost neutral. I'm not sure theres a good sized market out there.
Still, this sites already delivering the goods and I'll support it no matter what the descision, oh and buy the SNES version of Metal Marines when it makes its GOG debut :) hint hint

1.Super Nintendo
2.Genesis
3.Toss-up between N64 and Dreamcast
The reason for the N64 not being placed definately 3rd is because so many of its greatest titles have been ported to other systems or updated with slightly modern graphics. The dreamcast is the most under-rated system of the century ;P and while it has many great titles, it does lack the variety the N64 has. So there's my reason for the tie.

1) Nintendo 64
2) Dreamcast
3) Super Nintendo
Tho the one I really want is the N64, all the others are just a nice to have. I know it's not on the list, but I'd love to see PS1 and PS2 games here. Especially the Silent Hill Series <3<3<3<3<3

1) Super Nintendo
2) Nintendo 64
3) Arcade

1. Super Nintendo
2. Dreamcast
3. Sega Genesis

1) Genesis/Mega Drive
2) Nintendo 64
3) Arcade

1. Commodore 64
2. Amiga
3. Sega Genesis (Megadrive)

First, my primary concern is that you won't be able to offer games from any of these systems without DRM and I really really strongly encourage you not to abandon that philosophy. I'd like to know what your stance would be on offering non-PC games with DRM. I also think it would be best if a purchase of a game from these systems would include the ROM separate from the emulator so that we could use the ROM in whatever emulator setting we choose.
As for the systems:
1) Arcade
2) Super Nintendo
3) Commodore 64
I think N64 would be too difficult to control using a PC interface (without hacking an old N64 controller). Thanks for allowing us input!