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

1. Dreamcast
I doubt any of the others will really catch on with the widespread use of emulators. Not sure how much financial benefit you would gain from the older systems. Granted, the same might be true for DC but it's something I, personally, would buy.

1. Nintendo 64
2. Dreamcast (I really really really really really really really really really wanna play Shenmue so badly.)
3. Arcade

Nintendo 64
SNES
Dreamcast

1. SNES
2. Nintendo 64
3. Sega Dreamcast
And even though it's not on there I miss the 3DO, had some great games and graphics were great compared to most things at the time.

1) Super Nintendo Entertainment System
2) Nintendo 64
3) -INTENTIONALLY LEFT BLANK-
I'm not really sure I like the idea of multiple systems on here. It just seems far too much like Gametap (and Gametap is horrible these days). On top of that, it's getting harder to find games I don't already own.

I'm content with GOG being a PC exclusive service, but, if you really want to add games from other platforms, I vote for Sega Genesis, SNES, and Neogeo.

1. C64 (Old school!)
2. Amiga (Old school, good graphics and good sound, and a lot of GOG too!)
3. NES (For those SMB 1 - 3 Games)
Edit:
Oh, and if you start to sell games of other systems, please keep the sites seperated (as in: gog.com = PC, amiga-gog.com = amiga.... you get the idea).
Else its going to be one huge mess in those virtual game board ^^

True. GOG has ordered their releases based heavily around publishers (which I can understand). And in some cases the approaches might amount to the same thing as some publishers concentrated on one or two genres. That's just an uneducated guess though.

1. sega genesis
2. super nintendo
3. er... arcade.

1. Sega Dreamcast
2. Nintendo 64
3. Sega Genesis
4th would be the Super Nintendo and its basically interchangable with the Genesis both were great systems for the time.

1. Dreamcast
2. Arcade
3. Neogeo

My opinion is that they really should prioritize the other home computer platforms, those are games that usually were made for keyboard and mouse (some amiga and C64 games used joystick though), so they would play very close to how they were intended on the PC, while emulated console games really play better on modern consoles than emulated on the PC, even though you can connect an gamepad to the PC.
And, I think the home computer systems are a bit underappreciated compared to the classic consoles, and the classic console titles do get recognized on xbla, virtual console, psn, etc., while the classic home computers get very little recognition apart from some C64 classics stuff, and the iconic C64 SID music.
There were so many home computer platforms in the 80's and early 90's, and i'd love it if as the libraries of as many as humanly possible were available on GOG.
Amiga/CD32, Commodore 64/128, Atari ST/XE, MSX, the CoCo 1/2/3 and so many more which don't get the recognition they deserve.

1. Arcade
2. Dreamcast
3. Sega

1. Amiga
2. Super Nintendo
3. Nintendo 64