Under Windows, there's a long-standing issue with ATH.EXE and AppleMobileDeviceService.exe intermittently locking up.
Once they lock up, iTunes will seem to run fine, but iTunes won't find your phone.
You can go to an administrator cmd prompt and kill these services:
taskkill /f /im AppleMobileDeviceService.exe
taskkill /f /im ATH.exe
net start "Apple Mobile Device"
Now you can run iTunes and wifi syncing should start working again for a while. The more annoying bit is that when these services hang up, they also hog a CPU core.
It's kind of ridiculous that Apple hasn't fixed this yet.--
AT&T U-Hearse - RIP Unlimited Internet 1995-2011