After almost a week with no wifi sync issues, the problem came back, as it always seems to. After trying a few things, I tried ST67s idea of simply unplugging and replugging in the ethernet to my Mac (like turning wifi on and off if you're connected wirelessly), and that fixed the problem instantly... Even if this is a temporary fix, at least it's a quick temporary fix.
I had really thought 6.1 had helped, as my iPhone had been connecting amazingly well ever since the update. Well, until this morning. I was trying different things to get my iPhone to sync (resetting my router, rebooting my computer), and the process also made my iOS 5 iPad disappeared from the devices in iTunes.... Until disconnecting my ethernet for a few seconds, that immediatley brought both devices back to being visible in iTunes, and syncing fine.
I'm starting to see the light to KHuhn's asserstion it's an iTunes/bonjour issue, perhaps barely related to iOS 6 at all...