I backup through iTunes...well, virtually never. That's no different at all from pre jailbreak, iPhone and iPad. I hate iTunes, it routinely eats music and videos I've purchased and leaves no trace of them on my hard drive, sometimes even off the device itself. It's ugly, kludgy feeling, and poorly laid out. And Apple's idea of "sync" too often means "erase device content and replace" with what's on the computer. Ugh.
I use a variety of other backup methods and they get done at different rates. Apps like Notebooks for iPad are backed up onto my hard drive using SyncDocs, which is a tool they've incorporated into the app for wifi (manual) sync. Notebooks and a couple of others are also routinely backed up onto MobileMe iDisk, again through built in app functions (a lot of apps will do this with Dropbox if you prefer). MobileMe also handles my Calendar and Contacts sync, over the air and automatically, so both devices always have the same data. So all the really critical data is backed up regularly. And unlike with iTunes, if a backup is corrupted, I can see that immediately, instead of when I'm trying to retrieve something in an emergency.
Everything else is backed up to the Mac using a program called Phone View. It's easily the best money I've spent in years. It will even allow me to export SMS and voicemail from the phone (which iTunes won't do), photos, music, or anything any app has saved with File Sharing--without using iTunes. Using this and the other methods means I can restore a device as new if I have to (the cleanest way if you're jailbreaking), and still be able to reload the content fairly easily.
Once in a while, I plug in and "transfer purchases", but again, only after those have already been copied to the drive with Phone View.
