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Originally Posted by Lotus Esprit
So basically if you upgrade after you jailbreak then you would have to wait for the new jailbreak and manually install all of your non app store apps again?
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Correct.
For minor version bumps (3.1.1 to 3.1.2) the jailbreak development team has typically been able to use the same exploits so a new jailbreak is released within days of the Apple update. But for the major versions (2.0 to 3.0) it took weeks, even with the developers having access to the betas. Apple tends to hold their final security locks for the actual release.
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No way to backup and restore from the original jailbreak?
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No. Not really. There are two components to what is in the memory, one is the OS and the other is the user-space data (songs, movies, applications). On an iPhone it's even tricker because you have baseband firmware (the cellular modem that connects to your provider).
iTunes only backs up official Apple applications and not Jailbreak applications (it doesn't even acknowledge their existence on the device really). So a backup and restore, even staying at the same version of the OS, doesn't restore them. You have to re-jailbreak and then re-install. Remember, Apple has no incentive to make jailbreaking easy.