"Arcade" seems like a pretty ambiguous thing to say, but:
1. Dreamcast (if not the Saturn)
2. N64 (Virtual Console coverage is pitiful)
3. Amiga or C64, equally (the VC has shown that computer games should be on a computer)

1.) NeoGeo
2.) Arcade
3.) no third preference

1) Neogeo We need some great fighters on PC, just add netcode and you're golden. May be tough to get SNKP to play bill though
2) Dreamcast
3) Saturn. Not a choice given, but a number of really overlooked games.

1: Dreamcast
2: Nintendo 64
3: Arcade

1. Neo-Geo
2. Arcade
3. Amiga

Dreamcast
N64
Arcade
Hardest to get anywhere else......

Maybe it's a good thing if SNES and N64 would come to GoG.
For the first time we would see Nintendo games offered on the PC (aside the Mario 3D head xD), and if the sales are stable, Nintendo would maybe consider releasing games for the PC.

Amiga
Commodore
Nintendo 64

1. Dreamcast
2. N64
3. Arcade

1. Amiga
2. C64
3. Arcade

1. Amiga
2. Arcade
3. Dreamcast

DREAMCAST!!!

1. Dreamcast
2. Amiga
3. Neo Geo

1.Nintendo 64
2.Sega Dreamcast
3.Sega Megadrive

Though Amiga had lots of good games and some games probably the best music ever made (e.g. Lotus series), I could not think of any game that would not be on PC or I hadn't played through already. There are some unique diamonds (like Chaos Engine), but still.
I did not know all these consoles, so I started to do some research and indeed there is a clear winner in this group while others are more or less uninteresting eventually. Though I would buy Paper Mario on N64 instantly, I did not find too many interesting titles. Besides, how many of the people are just voting their favorite platforms from the childhood without thinking if they would actually pay for those games again, my guess is too many (in that case Amiga would surely be on my list too)
The one and only, number 1, 2 and 3 is... Sega Dreamcast!
I started to see the list of games and my GOD there are many interesting games I've never heard about, but would like very much to try! If you can get at least some of those "for Japan markets only" (especially role-playing) titles playable on PC, you will become my personal heroes for sure.
If You forgot, I repeat:
1. Sega Dreamcast
2. Sega Dreamcast
3. Sega Dreamcast
I have spoken. He who listens and understands these words, will find Wisdom and through Wisdom comes a gigantic pile of dollars.