Everything should be left as is except, of course, for OS and UI changes due to the update. You might find that an app you have installed is not compatible with with JB, but likely they'll be OK, most apps have been updated by now.
Of course you should always, ALWAYS have backups of important files at all times.
Linux user #266351. Android since v1.0
Registered Linux user #266531 since 2001. Android user since v1.0.