Plug the phone in with the cable and let iTunes back it up. In the process, it will recover crash log information from the phone and squirrel it away in Library/Logs/CrashReporter/MobileDevice/<iPhone or iPod name>/OmniFocus*.crash (in your home directory) -- mail those files off to
omnifocus-iphone@omnigroup.com and get a diagnosis.
I had some similar problems with a database which was blatantly too large (12k+ actions) when I started. The iPod was able to download the file, but then would crash before giving me a chance to do anything. I would tell iTunes to remove the OmniFocus app, sync, have it reinstall it, sync, and try again (after paring the database down some more). I eventually got it down to a size where the startup sequence would complete, and it has been happy ever since. There's no way of telling from the information that you provided that this is your problem, so I'd recommend that you take the former approach (or call them at 1-800-315-OMNI).