1.Amiga
2.Dreamcast
3.Neogeo
I would say arcade but MAME is just so easy and there is too much risk in getting complete crap on the site given the wide variety of dung available on Arcade platforms.
Aside from that Amiga, Dreamcast, and Neogeo have more RPGs!

Super Nintendo
Nintendo 64
Arcade
This probably aint popular.....but heck its childhood....(Mario 64, Super Star Wars, and Galaga, spring to mind)

Amiga
Commodore 64
Sega Genesis

1) Amiga
2) C64
3) Dreamcast
My third choice would be Atari ST, except it's not on the list

1) Amiga (if not Atari ST)
2) Sega Genesis (Megadrive),
3) Arcade

Nintendo 64
Sega Dreamcast
Super Nintendo
I would really love to see titles like "The Legend of Zelda: Ocarina of Time", "The Legend of Zelda: Majora’s Mask" and many other classics on GOG!
Please make it happen!

What happened to the Dreamcast was the result of several factors.
1) Bernie Stolar was a moron
2) Consumer confidence in Sega was at an all time low because of the failed Genesis add-ons and the premature demise of the Saturn.
3) First party titles were strong but third parties simply ported from the PSOne making the console look graphically inferior to the PS2. Which it was only marginally.
4) No online titles at launch despite being marketed with 6 million players. 6 months after launch we finally got Chu Chu Rocket.
5) No support from EA. Despite what you think of them they are important especially in the US. Sega had to divert a significant budget into Sega Sports to compete with Madden and NBA.
6) The 33.6k Modem was not fast enough and only Quake 3 managed 4 player online play with any level of smoothness. Unreal Tournament was cancelled.
7) A vast majority of players were happy with the PSOne and were prepared to wait for the PS2.
There are other factors but those are some of the biggies.

From what I've heard, the Saturn was a very oddly made system that is hard to emulate.

1 - Sega Dreamcast
2 - Genesis/Megadrive
don't care about the rest :P

Wouldn't moddability just boil down to the same ROM hacks that people already make? GOG would just be hosting an .smc, .iso, or whatever bundled with an emulator, I would think.

No it's relatively easy as long as you have the relevant ROM sets. The Amiga also had a unique hardware design but WinUAE does the job.

Dreamcast, N64, and Genesis I guess. Though it's not on the list, I'd vote for PSOne, as there were some frickin' awesome games on there.

Hm, good point, would they just create an emulator for the games or try to turn them into a PC port?

1 Genesis/Megadrive
2 SNES
3 Arcade