Besdie the persoanl taste, I have to disagree, you surely missed something about "old time" gaming.

1) Sega Dreamcast
2) Nintendo 64
3) Super Nintendo
Also, while it could possibly mean additional difficulties to get licenses, the possibility to easily detach the "data" (ROM dump / ISO image) from the emulator part for use on other OS / emulators would significantly increase the appeal of each release for me (assuming you'd go for a working-out-of-the-box approach, with no need to get additional software).

Well, i have an answer here.
first, Atari ST and Apple II good games were all amiga ports, so there is no real reason to get this specific version.
Older Apple games were monocromatic, dont think they could have any appeal today.
About the edit.. GOG can spend any energy but it will be quite impossible to have drm free EA/Activision games here, some publishers like blizzard will never sell outside of their sites for sure, so forget Diablo or Bioware titles.
You have to consider that GOG will not have in catalog everything listed in the wishlist, and "good old games" at a point will need to became not old, or not good, if they want to add something, so looking into older game platforms could be a way to offer more conserving the spirit of DRM free retro gaming.
Also, i have to add a line, some ppl seem to ignore that 90% of late 1980 / early 1990 pc games were amiga ports, where the amiga verison was far superior to the ported pc one, so having the original amiga one imo could be very welecome.

1: SNES
Just way too many classics; Super Mario World, Super Mario World 2: Yoshi's Island, Super Mario All-Stars, Mario Kart, A Link to the Past, Chrono Trigger, Secret of Mana, Secret of Evermore, Super Street Fighter 2 Turbo, Bomberman 1&2, Star Fox, a whole load of Final Fantasies, Lufia 1&2 and I'm sure I'm forgetting a lot too...
2: Dreamcast
I just want to play Skies of Arcadia.
3: Amiga
Back in the early days, "the Amiga version looks better than the DOS version". I would love to experience that.
Good runners up:
Sega Master System and Sega Mega Drive/Genesis for the boatload of good Sonic titles.
Nintendo64: Super Mario 64, Ocarina of Time, Goldeneye, but that's just the top 3.
Playstation 2 had, in my eyes, the best line-up of games ever, but is probably too new.
Arcade, because I missed out on that completely

1). Amiga
2). Commodore 64 or Atari 65XE
3). Arcade - geeez, I would do anything ( well, almost ) to play a Flying Shark and Raiden :D

1) Amiga
2) Commodore 64
3) Dreamcast

1. Sega Genesis
2. Commodore 64
3. Amiga

My original message got butchered.
1. Amiga - due to the Koei games that were also better than the DOS versions of same at the time.Genghis Khan, Nobunaga's Ambition - amazing. Lemmings, Cannon Fodder and SWOS were pretty fun too.
2. SNES - updated Koei games, Front Mission 1.
3. Dreamcast- it would make Gog completely unique and has a big library of really good games esp. beat em ups. Tokyo Extreme Racer series was a lot of fun. The last console to really have character.
4. N64 - Goldeneye & Perfect Dark. I feel this is less important since Goldeneye is being remade for Source but I don't know of a Perfect Dark mod.
Not listed: Playstation 1 & 2 - Front Mission series (including and especially FM5). Koei's naval series.
Saturn - some epic fighting games. How I loved Figthing Vipers.

I think it is not a good idea to offer games for anything but PC. How many people does have 8 bit computers? This will only take reosurces from adding more excellent PC games.

1. Amiga
2. ZX Spectrum
3. Commodore 64

Sega Dreamcast
Sega Genesis (Megadrive)
Nintendo 64

I'd prefer Gog.com to concentrate in PC games (you're just getting started with your current selection of titles), but if you guys have resources for something extra, then my choices are:
1. Amiga
2. C64
I don't much care about consoles, only the latest models of the 21st century have succeeded in making me somewhat interested, but most of their games I don't like at all.

Personally I find it hard to believe that you could run out of choices for GOG considering how many titles have been released on the PC in the last 15 years. I am perfectly content with my PC choices both "old and less old." Also I'm not much of a console fan but if I had to choose 3 from your list I'd have to say:
1. Amiga
2. Nintendo 64
3. Sega Dreamcast
Here's to hoping though that some of the more popular wished games appear here though before any console port.

1. Amiga
2. Commodore 64
3. Mega Drive/Genesis
A little about my choices. Both Amiga and C64 are computers, so their games will usually work well on PCs. They're also great machines, with loads of classics, and have emulation platforms that will let GOG create DosBox-like installers.
(also, some of GOG's partners have a great lineup of both C64 and Amiga-titles to pick from, Rebellion seems to be a treasure chest, for instance)
I picked Mega Drive simply because SEGA are already involved in digital distribution of their old games on the PC, and I think they could be a great partner for GOG, and bring in a lot of new customers.
Also:
I want to be clear that I'd like to see these platforms added IN ADDITION to the PC-games on GOG. In other words, if GOG starts to routinely release games for other platforms, I don't want the result to be LESS PC games. A good solution would be two PC games and one "other" game per week, for instance.

1. Nintendo 64
2. Dreamcast
3. Amiga