first and foremost you cannot update and remain jailbroken. you are removing one firmware and replacing it with another
now, since you will be losing the jailbreak my suggestion would be to restore as new/set up as new phone when given the option after selecting "Restore" in iTunes. do not restore from a back up. obviously this option is completely up to you but i have found that this will eliminate any issues/imperfections that you might of had from your previous JB. as you probably already know this will wipe the device clean and restore it back the original settings, except with the newest iOS of course
before doing this i would also highly suggest taking screenshots, writing down or using some sort of backup/restore app regarding all of your jailbroken apps & tweaks. i prefer writing them down by going to the Packages section of Cydia. i have also found by doing this you can eliminate a lot of things that you may have tried and never used again
restoring as new can definitely be time consuming but well worth it in the end..
i'm not a big gamer so saving game data is not a concern for me, although it can be backed up if needed
SMS can be backed up if needed (google is your friend) i never save my texts so it was not of any importance to me
i backup my photos to my laptop and email them to myself, this is when i really decide if i "need" them on my device or just keep them saved
apps & music can be easily put back onto the device, as you know
notes; not concerned but i'm sure they can be backed up and added at a later time
emails; i have 6 accounts. when i first started restoring as new i would take screenshots of the vital info for each account and email them to myself so re-adding accounts was less painful... now i can do it with my eyes closed
contacts and calendar... i sync both with google sync. very convenient
lastly, you may want to investigate the idea of upgrading all together. i have read many reports of users not happy with the 4.3.x builds and wished they could go back to their previous OS. this can ONLY be achieved if you have saved your SHSH blobs with TinyUmbrella or by selecting the "make my life easier" option in Cydia at one point. saved blobs will show at the top of the main page in Cydia
my suggestion before doing any of this, especially if you are happy with your current set up is search-search-search.. this forum, other forums and google before doing anything
hope this helps