In short,
There is no easy way.
There are apps that will "backup" your jailbroken info, but those tend to fail sometimes and are not totally reliable.
My advice:
1. Backup with iTunes (disable iCloud).
2. Backup with iCloud (just for kicks but either this or iTunes will do).
Now buy* from Cydia PKGBackup or AptBackup (*don't remember if these are free).
Use them but NOT to backup your apps, only settings, I don't remember beforehand but one of them basically tries to save your Cydia app preferences. The other does that and/or saves a list of Cydia apps as well and once you run them in the "newly" installed iOS version it can automatically download them all for you (DON'T do this. It sucks and sometimes you end up with a messed up jailbroken iDevice).
Now, what I'd do if I was to jailbreak again (haven't because I'm without a computer right now at home), I'd save files from these locations (I have them bookmarked on iFile, don't remember exactly why, but they were important last time I checked):
/var/mobile/Library/Preferences
/etc/apt
/var/lib/dpkg/info
/var/mobile/Library
/var/stash/Applications
/var/stash
/var/mobile/Libraries/Caches
Save them via SSH.
Then make a list of your Cydia apps (pen and paper).
Now you're ready.
Update to new iOS, jailbreak.
Now re-download apps from Cydia (your paper list).
You're almost done.
Use one of the backup apps I mentioned to recover your Cydia apps data.
If it fails or some didn't click (and some definitely won't be backed up as themes and so on), then I'd take my old backup (made via SSH), inspect what I need and once again via SSH copy it back.
Now it should work just fine provided the Cydia apps work on the new iOS version (sometimes you will need to find replacements if you have 4.x outdated apps).
As you can see, it's easy as pie but boring as hell.
Have fun.
