1- SNES (Chrono Trigger > everything)
2- Sega Genesis (the games in my childhood :)
3- Sega Dreamcast (because they're too hard to find)

Dreamcast
Nintendo 64
Super Nintendo

Nintendo NES, because it's a myth.

1. Dreamcast (The graphics still hold up to semi-modern standard as well as I never got to play with the real console much)
2. Sega MegaDrive (ALTERED BEAST! GOLDEN AXE! SONIC! Ok so I'll stop being silly, basically nostalgi. This was my console I grew up with until my parents threw it away... The only day of my life I hoped I was adopted)
3. Amiga. (So many fun and interesting games.)

Amiga: The underground comunity is quite big and willing to pay for those games. It might be complex and a lot of work to get licenses for most of the titles, but there are games (such has cadaver) that are worth the pain.

I would go for
1. Amiga
2. Arcade
3. Dreamcast
I would love to add the SNES, but it is very easy to emulate and therefore probably not as hot a seller as one might think. Also, mine still works :D

1. snes
2. nintendo 60
3. sega gen

1. C64
2. Amiga
3. Arcade

Amiga mostly. I long to play Chaos Engine in full screen.
Arcade games would be second.
Although i'd be happy seeing more DOS era games being put up.

1. Amiga (Graphics and sound were superior to pc versions. eg: F19 Stealth Fighter, Indianapolis 500, Eye of the Beholder series)
2. C64
3. ZX Spectrum (Chaos, Tau Ceti, Tau Ceti Academy)

Since the list offers certain choices:
Neogeo
Amiga
C64
I wouldn't care for Nintendo systems as I already have a Wii and where they are charging $8 for old SNES games I doubt they'd let someone else sell them online for cheaper.
But I would really prefer things that aren't on the list:
Atari 800
Atari ST or Falcon
Atari Jaguar
NUON
TG-16 (for cheaper prices than they do on WiiWare)
3DO
Phillips CDi
Sega Saturn

Dreamcast—It's a great system and it'd be cool to have better access to these games
Arcade—Would love to have access to quite a few there, but it's really a wide range of games there.
I have no real preference for a number three. Although playing Contra Hard Corps on the Genesis (Master Drive) would be quite fun.

1. N64 (especially "Rogue Squadron" and "Legend of Zelda: Ocarina of Time")
2. SNES (starting with the old-school Mario series)
3. Sega Dreamcast

Macintosh
and Apple ][! Old school Apple FOREVER!
the Apple ][gs also had some good exclusive titles

I'm assuming some of them are just jokes?
The Atari 800 was only ever big in the US (thats being generous)and it missed a lot of the 8-bit renaissance that Europe had with the ZX Spectrum, C64 and Amstrad CPC. Believe me I know, my parents bought me an 800XL and I had to hunt hard for games in the �1.99 Mastertronic range.
Atari ST was inferior to the Amiga in almost every way. The long running joke in schoolyards was that people who loved the ST couldn't afford an Amiga. There were a handful of exclusive games and even ST games like Dungeon Master were improved when ported to the Amiga (stereo sound). The ST was a superb music sequencer however. First and only console with MIDI interfaces IIRC. Falcon had even less support. Amiga 1200 Killed it.
Jaguar again was undersupported. Mostly it had Amiga CD32 ports like Syndicate and Cannon Fodder. There aren't many reasons to own a Jaguar. Tempest 2000 is the most compelling one. It's just a format that has no commercial interest and is therefore below the ZX Spectrum on emulation wishlists.
NUON - Thats a joke surely?
TG-16/PC Engine no complaints. One of the best versions of R-Type, not to mention Atomic Robokid, Gunhed and Devil Crush.
3DO - You will run out of games in one month. Road Rash, FIFA, NFS, SSF2TX, Wing Commander and then you seriously dip in quality.
Phillips CDi - Again this must be a joke.
Sega Saturn - Wholeheartedly agree.
I'm not wanting to have a go at you but saying you would prefer the NUON or the CDi to the Amiga, Dreamcast or C64 is just bonkers.