Completely wrong. Sega for example own all their IP's to this day. There is a legal grey area where some have claimed if you own the cartridges then you can also own a ROM back up. I say this is a grey area as to do this you have to break whatever encryption is on those cartridges. ROM sites exist because the site owners own the ROM's and they archive them in this manner to allow others to have these ROM copies. However the simple fact is that 90% of the downloaders don't own and probably never have owned the cartridges.
Emulation however is 100% legal UNLESS said emulator like WinUAE or SSF requires a OS ROM which you have to buy from the copyright owner. In the case of WinUAE this requires a Kickstart ROM which can be purchased with Clonato's Amiga Forever package under licence from Amiga Inc.
So no all the copyrights will hold up in most courts and companies like Nintendo have been very aggressive in their protection of them.

1. Sega Dreamcast
2. Arcade
3. Nintendo 64

I have to say that it's a bit backward-thinking of you to imply that an open-license project can't stand up to a professionally-made one. In fact, I would make the argument that a bunch of guys with no deadlines and a love of programming that keeps them motivated would often make a much better product than someone who is on a strict time line to push a product out the door.
Hell, I remember back-in-the-day when Sierra would push out a buggy-as-heck game, having to release patches only weeks later to make it playable. Meanwhile, the fine folks at AGD Interactive pushed out an almost-flawless remake of King's Quest on their first try for free.
And the guys that make the emulators for the newer systems don't need Nintendo or Sega's help. They already got their logic analysers out and reverse-engineered those systems a lot time ago. The reason they're glitchy is because N64 and PSX Rendering Calls don't translate 1-on-1 to DirectX.
For a final thought, don't forget about two of the most significant open-source made projects of all time: Linux, and Mozilla Firefox. They are both open-source, and have stood up to the two juggernauts of the technology world (MS and Apple) for more than a decade.

1. Amiga
2. Commodore 64
3. Arcade
If there was a 4th choice I would end up choosing Sega Dreamcast.
Indeed it's kind of a waste saying Nintendo / Super Nintendo or the first PlayStation because they have their own virtual stores, be it on the Wii or on the PS3. Still, I would love to have these 3 platforms on GOG... Just imagine all the NES / SNES and PS games here. :)

C64
Amiga
Arcade

1. Amiga
2. Dreamcast
3. Commodore 64
I say Amiga first, because I think it has a lot of historical significance, especially in Europe, and while emulators and roms aren't uncommon, they aren't the easiest to set up, and doesn't give the games the historical context I think a GOG release would (both with a preconfigured GOG wrapper and great background info on the GOG site), and I think the Amiga, even more so than the C64 influenced the modern PC games. It was the first common home PC with rather advanced graphics and sound hardware, and was a valid competitor for the IBM PC up until the mid 90's, with many great games in it's library.
I'd especially want to see some of the Psygnosis games which really utilized the graphics and sound capabilities to it's fullest (while possibly lacking somewhat in gameplay), and games like Gloom which I think is one really interesting Doom clone.
I put Dreamcast second. Personally I'm not _that_ interested in the system, and probably wouldn't buy many of the games, but it was an important system, which had a too short life. It would really deserve to have it's titles re-released on GOG or modern consoles.
And well, I also chose the Commodore 64. I have no personal connection to that or any of the other machines I mentioned, but the C64 glory days were a couple of years before I was introduced to gaming, but still, it was a very influential machine, especially when it came to music and sound, and how it gave birth to most of the demo and cracking scene. Possibly not a part of computer history that publishers want to give too much attention, but demos, cracktros and demoparties were really important when it came to computer generated art, and several demo groups later became important in the gaming community, many as developers (Remedy was founded by former Future Crew, Starbreeze created tracker sequencer programs, many vgm soundtrack composers are former demoscene musicians, like Alexander Brandon, Jesper Kyd and many others).
Sorry, this post went on a bit too long. :)

They don't need their help but they would be infinitely better with it. Compare Super Mario 64 running under emulation on the PC and then compare it to the Wii version. With emulation there is often a lot of guesswork involved, the programmers know how the hardware works but not how any embedded ROM OS makes it work. This is why some of the best emulators like WinUAE can use official Kickstart files to make the whole process smother. Despite the power of the average PC there is still no 100% PS2, XBOX or GameCube emulator.

1: AMIGA!! - Yes, I have to shout because its that awesome and its clearly not a popular enough vote yet :D
2: C64 - First platform me and my bros owned. Back in the day I never read mags of anything so I had no idea what the great games of the commodore were. Apart from Turrican 1+2 and the Dizzy games, I don't think I had any of them. To be honest I still don't know what most of these greats are! lol
3: Arcade/Dreamcast - Its a toss up between those two. I have older Nintendo and Sega consoles thanks to emulation, I never got around to collecting mame stuff, and I haven't even considered a Dreamcast collection. They both have some interesting games that I wouldn't mind owning.
I agree with what Aliasalpha said, I would rather buy the games in packs and not pay that much. Mostly because during the last few years when Midway or whoever would sell their classics collections, I'd look at them and think "I have hundreds of nes, master system and mega drive/genesis games all burned onto 1 CD, and those lazy gits put 10 or so games onto a DVD!! Thats a waste of a disc, I'm not buying that shit! They could have stuck every single one of their games from a specific generation on there, with a shitload of stupid extras. Then I would have been a little more interested."
I'd also like to see people doing what Capcom did with Street Fighter 2 HD Remix with their games. A Nice facelift, rebalance the game, fix issues etc, but still keep its original form.Depending on whats been done, I still wouldn't want to pay to much for that either though.
As for the Amiga, I would be a little more interested in physical copies so I can play them on my Amiga, but I'm not too bothered by this.

Amiga / Commodore 64 - never played one of their games, but I'm interested in them
Sega Genesis (Megadrive) - including games for Sega CD and Sega 32X
Arcade
Not in the list, but I want to see some MSX games also

1) Arcade
2) Amiga
3) C64

Super Nintendo
Nintendo 64
Sega Dreamcast
Nintendo has a lot of great titles. Secret of Mana, Breath of Fire, Final Fantasy, Zelda and Castlevania just as a few examples.
I still don't understand what happend to the Dreamcast... Awesome graphics, modem, web-browser, mouse and keyboard (!!!), really good games, great ideas and a lot of other stuff to add to the console. Some Indie-developers are active until today! So what happend ten years ago? Why did it fail so badly? Today people are happy with extremly overpriced hard disks, paying for XBox-Live and playing FPS with a controller. Was the Dreamcast to good to be true?
However... It has some good games and I missed most of them because the Dreamcast failed badly in my region.

Amiga
Dreamcast
Arcade

Amiga, SNES and NeoGeo.

I would pick Amiga, C64/128, and although it's not on the list, the Atari ST. For a platform that is on the list, however, I would pick arcade.

I vote:
Amiga
Commodore
Dreamcast
In no peculiar order. Amiga and commodore are obvious choices. But Dreamcast is a personal demande, for I've often heard praises for the console and its games but never really got the opportunity to try them.