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AirSharing uses Bonjour networking over WiFi to send and receive files. There are a number of other apps that have been using this implementation since the app store opened (SplashShopper is an example. Things is another).

OmniFocus could do this also if they built that functionality in. In fact, OmniFocus uses Bonjour networking over WiFi to send the settings from the the desktop app to the iPhone in order to set up syncing initially. The main problem with this approach is that you can only sync when your computer and iPhone that are trying to sync are on the same network. The primary advantage of Bonjour networking over Wifi is speed and ease.

To date, OmniGroup has chosen to keep syncing in the cloud. That way you can sync regardless of where you are (as long as you are connected to the Internet in some fashion).

For me, the current implementation is working pretty well (after a few hiccups initially). I'm syncing 2 Macs and 1 iPhone.