Castles & Crusades, because that was Gary's intention, and I think C&C fixes most of the mechanical problems with earlier D&D while maintaining the old school feel. Of course, if CZ was released for something like 1st Edition AD&D or classic D&D, it would still be easily usable with C&C!
OD&D or 1e/AD&D would be my preference, even though I'm most likely to actually run it with 3.x. I think keeping it closest to a system E.G.G. actually used and was familiar with would work best with a minimum of mechanics futzing in development.
Voted 'other' - Labyrinth Lord just pips out C&C as my current preference. I have a few too many issues with C&C:
Saves are too hard, esp at high level.
This makes casters too powerful.
Casters get too many spells.
Some spells are way overpowered (Sound Burst), prob due to poor editing
Likewise, poor editing gave rise to ridiculously overpowered items like the Ring of Evasion
LL has none of these editing or design issues, and includes all the spells I want.
I voted AD&D first edition, but really, any of the systems in the "TSR D&D and simulacra" family would be all right. Cross-compatibility is high, and they share a similar design philosophy/implied play style.
I would not feel comfortable with a 3e, 4e or LA version; Zagyg just isn't for those kinds of games.
I voted 3rd Edition for the very selfish reason that I'm using that system. More logically, the OGL makes it a more appealing choice for some to publish it that way, but I'm not sure how well it would sell to a 3.X market, or how heavilly they'd change it to match the design ethos of such a product. Part of the charm of Castle Zagyg would be having as close to the classic Greyhawk dungeons as possible, and that doesn't necesarilly include some of the stuff tied into the 3.X rules.
To be honest, though, I wouldn't be too fussed. Releasing it in AD&D 1st edition feels "right" to me, since that's what people expected when it was first announced, although I'm not sure how realistic it is to expect an OSRIC version of it. Castles & Crusades isn't a system I've ever felt a huge urge to look at but it was what the castle started as and, to an extent, the system only exists as an avenue for Castle Zagyg to appear - it'd be nice for previous customers if it could come out like that, though I really doubt we're gonna see that.