1. Sega Genesis
2. Super Nintendo
3. Nintendo 64

1) Sega Dreamcast
2) Amiga
3) Sega Genesis

1. Neo Geo and Arcade
2. Sega Dreamcast
3. Super Nintendo

1) Amiga
2) C64
If I had to pick a third I would say the Atari ST instead of the allowed choices. Oids, Sundog, and Star Raiders I would surely pick up if available. Star Glider and Time Bandits I really enjoyed too, though both of those were also available on the Amiga.
I would think that the Nintendo systems coming to GoG would be unlikely, since Nintendo is putting those out themselves on their Virtual Console on the Wii and DSi. If GoG could pull it off though I am sure there would be some titles I would purchase.

1. Sega Dreamcast
2. Neogeo
3. Nintendo 64

1. Sega Dreamcast
2. Amiga
3. Arcade

1. Dreamcast - This is nearly impossible to come by.
2. Commadore 64 - I've especially wanted to be able to play Wasteland for a good while now.
3. Nintendo 64 - As someone else pointed out earlier, Rareware is too difficult to come by.

Not sure if Microsoft is nice enough to release its games online, at least on someone else's site.

1. Amiga
2. Commodore 64
3. Dreamcast

Is the reason you don't have any Atari consoles listed because you already have Atari on board? Does this mean we'll finally get to witness ET in all its glory?

1. Dreamcast
2. Nintendo 64
3. Amiga

1. Super Nintendo by far
2. Genesis
3. Arcade

1. Amiga
2. Commodore 64
3. Sega Dreamcast

1) Commodore 64
2) Amiga
3) ?
My reasoning: Nintendo's got some pretty good retro-gaming contracts going on the Wii's virtual console. So if I need non-PC retro-gaming, I can go there. They've got all the Nintendo consoles covered and some of the Sega, and a few other companies have jumped on there. But Commodore and Amiga are most like PC gaming anyway, and some companies I like (such as Sierra) did some work on those that I'd like to see here. I don't think GOG would benefit from trying to compete with Nintendo for emulation.

1. Amiga
2. Neo Geo
3. Dreamcast