Let's say I have a jb 3.2 full of PDF books movies and many apps that were app synced in and some purchased apps. So if I update to 4.2 this fall what will my iPad look like after the update. Books movies photos and purchased apps will remain and the unpurchased apps will be gone and there space freed up?

I would not attempt to upgrade directly from a jb iPad. it's a possibility that it could brick it. instead if you must upgrade, back up your iPad, restore it to default using iTunes, upgrade that, and possibly apply a new jailbreak (one for the os version you are now running.)

How do I backup my iPad?

Just connect it to iTunes. It should back up automatically.

But be forewarned the backup does not backup everything.

1. Music, Video and Photos originally loaded via iTunes must be natively stored on your computer. If you have these only on the iPad and deleted off the computer since you first put them on the backup will not include this.

2. Obviously jailbroken apps must be transferred via iTunes via transfer purchases (assuming you are naughty and have done this

3. Cydia apps will not be backed-up, but Cydia should have record of what you had if you allowed Cydia "to make your life easier"

4. All manually loaded files loaded via jailbroken apps into your downloads folders (like movies in UlimVideos, or music via dTunes etc) are also not backup up.

Just a heads up

Yeah it will be a pain, but worth it when 4.2 comes out. Even if I have to deal with no jailbreak for a little while the new features will be well worth it.

Just save the movie files to your books and movies to your computer first.