I have read many reports of people having lots and lots of trouble with appsync and aptbackup. After hearing such reports I deleted aptbackup...I keep notes and have emailed screenshots of the packages from cydia that I have installed. Its a slow way to recover but it's better than the alternative.
I restored my iPhone on 3.0 using aptbackup and I can pretty much say that it bricked my 32GB 3GS. It would not restore and I had to get a replacement at Apple. Do not use aptbackup.
I used aptbackup when I updated to 3.0.1 from 3.0 and it installed most of the cydia applications, but hid all the AppStore applications and I couldn't restore their icons. I had to restore the phone and install the cydia apps one by one.
I've used AptBackup with 3.0 about 5 times... ONE of those times it caused the phone to not boot, and I had to put it into DFU mode and restore (this was also from using the backup from a different phone). So basically, it's certainly worth a shot, even if it's not foolproof.