1. Amiga
2. Super Nintendo
3. Nintendo 64
I'm not completely sure about 3, though. I'm kind of leaning towards the Megadrive there.

1. Commodore 64
2. SNES
3. Dreamcast

1. Dreamcast
I still love this machine but it' so hard to find anything for it at anything near a reasonable price.
2. NeoGeo
Who didn't love this thing?
3. Arcade
I can't even imagine how much money I dumped in my local arcade as a kid...

1. Arcade
2. Sega Dreamcast
3. Commodore 64
4. Amiga

1. Super Nintendo
Mario World, Mario RPG, Link to the Past...This system honestly had some of the best games of all time.
2. Nintendo 64
While the amount of awesome games wasn't as high as the SNES, the good games were truly kick-butt. I mean...Who hasn't played Super Mario 64, or Ocarina of Time?
3. Sega Genesis.
I dunno, just because everyone else is putting it on the list. I never had one nor really played one before though.

1. SNES
2. Nintendo 64
3. Neo Geo

1) Dreamcast, it is the best console of all time, no challenge.
2) SNES, another great console with some unbelievably great classics, especially RPGs (be it Square or Enix or both).
3) I'm undecided between Commodore or Amiga, both have really good games.

1. Nintendo 64
2. Dreamcast
3. SNES

1. Sega Genesis
2. Sega Dreamcast
3. Commodore 64
Of course, Genesis and C64 would be easy because the emulation is almost perfect nowadays. Don't know about the Dreamcast though, the only game I've ever emulated was Ikaruga ... and that was just to see if it would work since I've got it for XBLA.
The Neo Geo Pocket and NGP Color ... and Wonderswan would be pretty cool too. :)
And ... of course ... arcade games.

1. Nintendo 64
2. Amiga
3. SNES

1: Amiga (grew up with an Atari ST, but Amiga was arguably better. (Still prefer the Yamaha synth over some of the samples that Amiga composers would use, though...) Would love to see Mad Professor Mariarti, Nebulus and Bloodwych available.)
2: Arcade (note that Neogeo is largely a subset of Arcade. And don't forget the occasional arcade cabinets which ran NES or SNES games... :P)
3: ... hmm, I dunno. maybe Dreamcast, if you can get a decent conversion of Seaman.

1. Nintendo 64
(I doubt you could get any first party games, but there were so many good ones by Rare)
2. Sega Dreamcast
(ahead of it's time with a horrible controller doomed many great games to unplayability)
3. Arcade
(so many games, just so many)
Amiga and C64 are runners up, but many of their games were ported to DOS, and there is already a strong emulation community.

1. Amiga
2. Commodore 64
3. Arcade
You can already play older Nintendo/Sega games on platforms like the Wii, what I think would complement gog's library the best would be the 80s computers: Commodore, Atari, Spectrum and so on. I would love to see some of the Japanese computers as well like the MSX and PC88.

1. Dreamcast - Ikaruga~!
2. N64 - many classics like Mario 64, Zelda, etc.
3. Arcade - lots of interesting titles, too many to mention.

1 - Super Nintendo
2 - Sega Dreamcast
3 - Nintendo 64