1. Arcade
2. Sega Genesis
3. Sega Dreamcast

Sega Master System
Sega Genesis (Mega Drive)
SNK NeoGeo

1. Neogeo - because it's under-represented on virtual console
2. Dreamcast
3. Arcade

Xbox (original)
Amiga

1. Sega Dreamcast, because that's the only platform on the list without an emulator that's worth a damn
2. Arcade, because that's the most annoying to emulate of the remaining platforms
3. Amiga, for no particular reason
I really don't think there's a chance of Nintendo letting SNES or N64 games be released on a platform that they don't control that would compete with virtual console on the wii. The only time I know of this happening where the game wasn't multi platform to begin with is Perfect Dark, and that only happened because MS owns Rare now. Otherwise I'd have SNES as number 2.

1) Dreamcast
2) Arcade
3) I'm gonna have to say Dreamcast again

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

1: Sega Dreamcast
So many great games Shenmue 1&2, NFL 2k1, Skies of Arcadia, Marvel vs Capcom 2, Soul Calibur, Grandia 2, Jet Grind Radio & more, sure some of these have been liscenced to be put on 360 but the omissions are still so good you guys need to jump on it before Microsoft nabs them and puts them on live.
2&3: Arcade & Nintendo 64, There's a ton of great arcade games out there I'm suprised it's hardly getting any votes, The only games for 64 you need to make are Goldeneye & Legend of Zelda: Ocarina of Time while there are other gems those 2 will be your main money makers (especially if you get the updated Master Quest for LoZ: OoT that was put on Gamecube)
All the other systems listed have easy to find emulators & roms, I think you guys should stay focused on PC games (Get Baldurs Gate 1&2!) and if possible maybe getting PS1 games.

Sega Dreamcast games may actually happen as Sega have announced they are bringing Dreamcast games to the Xbox360 and Playstation 3 link

1. Amiga
2. Commodore 64
3. Nintendo 64

1.)Sega Dreamcast
2.)Sega Genesis
3.)Neogeo
Too bad Sega CD and PC Engine aren't options! Anyways, the Dreamcast has my favourite game collection of all time outside of the PC. With games like Shenmue, Virtua Tennis, Skies of Arcadia, Power Stone, Soul Calibur, ChuChu Rocket!, Space Channel 5, Typing of the Dead, Sakura Taisen, Ikaruga, etc it's hard to see how you could go wrong with either variety or quality. And if would be incredible if online worked too. Also it sure would be neat if you could get unreleased games like Propeller Arena!

1. NES (not on list I know, but can always hope)
2. Nintendo 64
3. Dreamcast

My Top 3:
1. Commodore 64
2. Commodore Amiga
3. Super Nintendo
Reasons:
1. The Commodore 64 is THE best selling, and most well-loved (hobby) computer from the '80s. While the manufacturer has since gone bankrupt and the rights to the company's products have been sold from one company to another (I think Tulip held most rights last I checked?), many Commodore users are still writing programs for it EVEN TODAY! This makes it the most long-lasting success from the entire computer industry. Many game concepts from todays games saw their origins in the Commodore 64 era. The space simulators found their origins in Elite, Escape from Castle Wolfenstein was a top-down 2D shoot'em'up before Wolfenstein 3D (its successor) decided to start us off on the 3D First-Person Shooter genre. Then there's the fact that Commodore as a company, and MOS as a chip manufacturer, couldn't have become as successful as they were in their haydays without the Commodore 64 to start them off. The Commodore 64's SID chip is still unsurpassed in terms of being able to compute audio data in realtime, even though Creative has made some headway into the area.
To summarize: The Commodore 64 is an ICON that brought with it not just games, but also a slew of amazing technology and (business) programs without which our current generation of home computers couldn't have existed.
2. Call me a Commodore-fangirl, but the Commodore Amiga continued where the Commodore 64/16/128 series left off. Great games, with some real mindblowing graphics for its day. I thoroughly enjoyed the Lotus racing game series, Sciv was great fun to play together with a friend, and Bar Games was a gimmick that should've had more of a fanbase. It was just great fun to have and play with. I personally own both systems listed in this; Commodore 64 & Commodore Amiga 500, and still enjoy playing with either. Just wish I had more space and more knowledge of how to preserve the original technology for the future. :/
A fun bit of trivia; For the longest time, the subtitles for many television broadcasting networks in the Western world were done with a Commodore Amiga, due to its ability to input these subtitles in realtime on a running video.
3. Talking about icons, the Super Nintendo really took the Nintendo Entertainment System to a new level. The games were amazing fun to play, but where the NES failed to deliver on the savegame section, the SNES brought gamers the option to save, go do something else, and then continue whenever they wanted to with the games they loved to play. I've fought many a round of Killer Instinct with my friends, and spent more time with that system than thinking about my homework. Much to the distress of my parents. ;)
Of all the Nintendo consoles, the SNES was the most succesful in my book.
As for why I didn't choose any of the others?
Sega took a wrong turn with their Saturn, and potential gamers took it out on them by dropping the Dreamcast before development was really complete. Sure, the Genesis was a great system, bringing Sonic and many other games into the world, and we must thank Sega for that. But they made some bad mistakes that are hard to ignore. The games on these systems WERE good, however, and their developers did what they could as the Sega brand sank into the quagmire they're in now. But having to work with their awkward controls might be a bit too much for the games to see new life as GOG games.
The Nintendo 64 failed, in my opinion. I know of few, very few, games that I liked on it. But the system didn't pull me to it as the NES or SNES did.
ANY arcade game is good. But only when it comes with the arcade system. Think about it this way; Terminator 2 was a fun arcade game because there was a large gun mounted in front of the screen and you could shoot the advancing hordes of T-800s with the gun in your hands. Playing it with, say, a mouse and keyboard, wouldn't be the same.
The Neogeo isn't a system I'm familiar with, and can't comment on.
Please do feel free to contact me about this reply. My email is makitk on the gmail network.

1. Nintendo 64
2. Sega Dreamcast
3. Arcade
To be honest, perfectly working emulators for 8-bit and 16-bit systems have been out for years, so unless you're able to give us some serious additional downloads for those games, you'll most likely not get too many bites.
However, the later consoles (N64 and Dreamcast, and the newer arcade games) would be different, and those would be worth while to have. :)

Fun Fact #2 The Pilot for Babylon 5 had all its CGI done on Amiga workstations.