I've noticed that windows hates itunes (well i kinda knew that for awhile..lol). Just tonight, my phone didn't want to sync right. Back up taking forever. Phone wasn't even indicating it was syncing but itunes thought it was syncing.
Unplugged the phone from computer. I basically had to turn the phone's power off by holding down the top button. Powered it back on. Closed itunes. Started windows task manager and stopped anything itunes related (about 3-4 things including itunes.exe). Restarted itunes. Plugged in iphone and bam, the sync took about 2min.
I'm not even going to try to determine what was the issue..be it the phone needing reset, itunes not liking vista over time, or vista. Who knows.. If a sync is really taking long, something is screwy somewhere. Usually my syncs are quick..