Thought I would share this link since I use it myself. I have a 64gb iPad and every time I would connect to iTunes to sync it would want to automatically backup. Since my iPad has tons of stuff on it, these backups would take well over an hour. You can use this free program (BackOff) to disable auto backups in iTunes:
http://www.digidna.net/products/backoff
Note that if you use this program you can still manually backup the iPad by connecting it to iTunes, right-clicking on the iPad and selecting "backup".