.mov is just a container, not a codec. A .mov file can contain video tracks of any variety of codecs (and audio track, which have their own selection of codecs). As I said before I have no experience with other software so I can't really speak for that, but H.264 is usually okay if you're only playing one on a computer. H.264 is extremely resource intensive so having multiple ones going never works out even on brand new high end Macs.
As for Macs vs. PCs, it's really about OS X not the hardware itself. A 5,200 RPM Mac Mini will play and sync an AIC-encoded video more reliably than most any Windows PC I've tested. Best advice I can give: don't be spec-obsessed.
1: There is no "headless" server option yet, although that's oft requested and I plan to implement it sometime in the future.
2: Not at this time.
3: I have no idea.
60fps would probably be fine on a newer Mac using Apple Intermediate Codec and flash storage. Haven't tested it myself.
Now is probably a good time to mention that there will not be any further updates to ArraySync, but rather a complete rewrite from the ground-up (and a rename/rebranding). Among the many improvements, I hope to switch the PC version to Windows Media rather than QuickTime, which should improve behavior on PCs greatly.