The only thing you shouldn’t do (at least not without some preparation) is update the firmware of your jailbroken iPhone. Firmware updates are relatively rare, aren’t exactly trivial and don’t run automatically without major warnings.

Other than that, you can do whatever the hell you like via iTunes without any precautions. And even if you do ‘accidentally’ update the firmware, you’ll rarely lose data and settings of jailbroken apps, just the apps themselves, and reinstalling those is a piece of cake (there’s even a nice little tool to backup your list of installed apps and re-install them automatically).