1) Nintendo 64
2) Dreamcast
3) SNES.
Realistically, I really can't see Nintendo agreeing to allow a distributor to distribute games from their consoles when they have the Virtual Console. That said, Sega may be more agreeable, and considering Mega Drive games are already on Steam and Gamersgate and confirmation that Sonic Adventure is coming to the PC, Live Arcade and PSN, the time to strike a deal with Sega is now.

My top choice would easily be Super Nintendo. One of the greatest console there ever were. All the classics by Square Enix, Nintendo's own games...
Besides that though, the Nintendo 64, while didn't have as many great games, still had some awesome games.
Adding actual consoles to GOG would be an awesome idea. Probably actually difficult to do (legally!), but it would bring a lot of people over here and be an extremely innovative thing to do besides.

My thoughts exactly. Everything else on the list is easily acquirable. And there are supported versions of most of the Nintendo games downloadable on Wii.
Having supported emulations of Dreamcast games would rock though.
To reiterate:
1. Dreamcast.
On the topic of games for Dreamcast, Gut's Rage would be awesome. San Francisco Rush 2049 would be great. Sonic Adventure of course. The Sega 2K football games were great on Dreamcast, possibly better balanced than even modern American football games. Skies of Arcadia was a great RPG. There are tons of games from Dreamcast that would be worth having...

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

1. Dreamcast
2. Genesis
3. Arcade
I'm a big Sega fan and a big fan of gog. If they were to come together it would be pretty incredible. Sega's Genesis games are widely available on other services but if it was a bigger selection than I'd be totally for it. Sega's Dreamcast titles on the other hand are hard to come by aside from the ones that have been ported to other platforms. And there are many Sega arcade games I have yet to try.

Considering that I own a Wii, and thus have access to their superb Shop Channel, I frankly don't find any of the alternatives listed very compelling. Arcade games might turn out to be interesting, especially since they're still being developed, but I don't see much point in selling a game that takes thirty minutes or so to finish.
Well, I guess the Dreamcast might actually be interesting. I hear it's got some pretty good games, and at this point anything Dreamcast is worth a fortune to buy used.

1: Amiga
2: Commodore 64
3: Sega Megadrive
Why?
1: Amiga has a lot of great games and it easy to emulate.
It has a wide variety of excellent adventure games, shoot 'em ups, platformers and strategy games, not forgetting simulator games.
2: Seriously, Commodore 64 is a worthy platform, it has got a lot of good games that many people keep on coming back to over and over again. And it is easy to emulate as well.
3: I chose this because I didn't really have a console of my own back then, but I think Sega has got a good selection of good games.

For me it would have to be the following systems
Atari ST/STE(FALCON)
Spectrum
Amiga

1. Commodore 64
2. Super Nintendo
3. Nintendo 64

1. Snes
2. Saturn
3. Dreamcast
4.Sega Master System
1. Earthbound. Earthbound, and Earth bound
2. Panzer Dragoon Saga.
3. JSR, JSF, PSO, countless other happy fun time games/
4. Because I wanna play a game where, as Rambo, my missions culminate in blowup innate walls.

Yeah, though I'm not sure dividing them by genres would really work (at least not if you mean cross-publisher bundles), my proposal would be either packaged by developer, and use the $9 price for developers with big collections and the $5.99 for smaller collections. If there are too many games or if the publishers don't agree, they could divide the collections by year of release or something.

This would be _the_ answer to legal emulation and a completely unique service to my knowledge.
I'd want as many systems as you can get your hands on. But given that I'm getting my Pandora, hopefully soon, I'd really love.
1. Sega Dreamcast (I own a bunch, but I lost my copy of Shenmue 2)
2. Nintendo 64 (Again, I own a bunch, but there's some I'd like to buy but don't fancy paying the eBay hawks' prices)
3. SNES (Own none of them. Before my time really. Tons of great games that I'd love to play)
4. Everything else, including Sega Megadrive. (Like I said at the beginning, the more systems you can get games for the better.)

Super Nintendo

Don't really care much about emulation, but please no N64. I can't seem to recall a game that has aged well on that system. OK, maybe the Zelda's, but if that's everything the system's got going for it ... .
If I need to make a top 3: dreamcast, amiga, neogeo. No particular reasons.