Sorry, I didn't read through the whole post. This is something I have been worried about when I upgrade to the jailbroken 2.2.1. From what I have read so far, it looks like we have to update to 2.2.1 through iTunes as a new phone and then do the jailbreak. I don't think you can QuickPWN an already jailbroken iPhone from version to version.
As far as TiPb being behind, they are usually the 1st or 2nd blog to update with new info or rumors. I can't imagine that they would be behind on a 2.2.1 jailbreak update.
It looks like AppBackup only backs up App Store apps, which would be beneficial since everyone seems to recommend against doing a restore from backup on a jailbroken iPhone. With AppBackup, you don't have to worry about losing app store data but I don't know if it works after you do a restore as new, because that removes the jailbreak, and I assume any jailbreak data. The only possible benefit I see for the app is that you can remove an app store app from your phone and then put it back on and restore the data.
AptBackup will backup and restore your apps from Cydia, but only the apps you have on your iPhone. It says it won't remember settings or placement, and can only be used after a fresh iTunes installation, not whenever you need it.
Let us know how the upgrade to 2.2.1 goes.
My additional questions are: (for Windows)
1.) I always assumed that restoring from a backup on a jailbroken iPhone was because Apple might somehow be able to track the jailbreak. Can they figure this out through iTunes?
2.) If you do a restore from backup on a jailbroken iPhone, does it remove the jailbreak and just put back all the non-jailbroken data back on it? Then you QuickPWN it again?
3.) Is there a way to update to the new OS, keep all the current App Store App data, call logs, etc. and rejailbreak?
(P.S.-Thanks for the clarification Bad Ash.)