1. C-64, because a lot of my favorite old games were on this platform.
2. Neogeo, because their games always seemed interesting at the arcade.
3. Sega Dreamcast, because there doesn't seem to be many Dreamcast games available (I bought most of the SNES and Genesis games I wanted off the Wii shop already).

Above all else, I'd want things from the Amiga, such as the Amiga versions of Team 17 games and the Lotus Esprit series from Gremlin. Oh, and of course Hired Guns too.
Other than that, the Mega Drive would be nice, especially if you could get the Phantasy Star games and Land Stalker, etc.
Now, if it were a choice, I'd love to see some Amstrad CPC versions of games. In particular, StarQuake =)
So in list form:
1 - Amiga
2 - MegaDrive
[3 - Amstrad CPC]

1. Amiga

1. Dreamcast
2. nintendo 64
3. NeoGeo

1. Dreamcast
2. Nintendo 64
3. Amiga

Commodore 64 and Amiga.
Because their classic games were designed to be operated with keyboard/mouse/joystick (I don't really like console-type game controllers), and I have those chidlhood memories.

1. Amiga
2. Commodore 64
3. Apple II
Mostly Amiga!

1. Dreamcast: I loved a lot of the games on the Dreamcast. Has the best Sonic games that ever went 3D and the Shenmue games are amazing. A console ahead of its time I believe. There's just so much I want to re-visit and play again and I'd love the opportunity to do it all again.
2. Megadrive: Epic Sonic games on it, plus loads more. I was a huge Sega fan back in the day and that hasn't died just yet.
3. Nintendo 64: The Zelda games would be great to play, along with several Mario games and a few more. A great console in itself. However I'm also torn between the Super Nintendo as well, but I choose this :p

Shadowrun FTW
But yeah:
1. SNES (My happiest console generation)
2. Genesis/Megadrive
3. Arcade (back when Arcades were where you went to play the best stuff)

1. Commodore Amiga - The very definition of good old gaming right there with some true classics. In the past I have mentioned the Amiga because once you go back before 1992 the Amiga was far superior to the PC especially in Audio. If GOG want to go back to older games then nine times out of ten the better version is the Amiga version. Just compare Xenon 2, Defender of the Crown or Dungeon Master. I always feel that with retro gaming you need the best possible version.
2. Sega Dreamcast - Despite losing out to the Playstation 2 the format had some legendary games. True it was flooded with some crappy PSOne ports but Sega's own games and games by Capcom were stunning. Power Stone, Street Fighter III Third Strike, Soul Calibur, Shenmue, Skies of Arcadia, Metropolis Street Racer and Crazy Taxi still stand up today. In fact Soul Calibur running through a VGA connector is still stunning to look at.
3. Super Nintendo - Just for the RPG goodness it's worth it alone. Add in Nintendo classics like Mario Kart, Super Mario World and Starfox and how can it not make a top 3 list? The SNES had a massive library of games and I would prefer it to the Genesis/Megadrive as at the moment if you want to play SNES classic you need a Wii or DS. Bringing Nintendo here would be a major coup for GOG. Assuming of course they realize a PC can be used for something other than calculating profits.
One question - No Sega Saturn? Sega PC already ported a lot of Saturn games to the PC but they are hard to find and they made a complete mess of the optimization. Last Bronx is totally unplayable without some way of throttling your CPU. Also I would pay a handsome price for a port of Panzer Dragoon Saga one of the best RPG's ever made. In fact I already did on eBay but PDS is one of the few games that won't work with a region converter cartridge >_<

1. Sega Dreamcast (Street Fighter III Third Strike, Darkstalkers collection)
2. Arcade (I want the the TMNT 2 arcade game)
3. NeoGeo (all the SNK fighters, specially Garou Mark of the Wolves and Samurai Showdown 3)

1. Nintendo 64
2. Amiga
3. Super Nintendo

1. Amiga (Wasn't a huge success in the States and it's a platform I've grown to love through research)
2. Neo Geo (The system has tons of great games that I would love to legally own on the PC)
3. Dreamcast (While I own one, games have become hard to find and I feel more people should be able to experience the best the system had to offer)

1. Sega Dreamcast
2. Amiga
3. Commodore 64