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I'm getting my iPhone swapped today at Apple. Is there anyway to back up EVERYTHING including all of my jailbroken apps?

If you PAY for PkgBackup in Cydia it can backup your JB apps. It saves them as a contact in your address book. Once you get your new device, re download PkgBackup then hit restore (after you have your contacts on your phone).
 
Use Pkgbackup for the jailbroken apps and backup to iTunes. All you need is to consolidate your iTunes library and copy that somewhere safe, and also copy your iPhotos folder, while also making a copy of your iPhone backup (you might as well just copy the whole iTunes folder).
 
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