One of the most frustrating things that I've encountered with the iPhone, is doing backups and restores. Now admittedly, most people are okay with this, they just backup their iPhone with iTunes and restore with whenever necessary.
I like to take the backup and restore process a bit more seriously. For instance, I've actually created a starting point "stock" iTunes backup with all of my favorite apps, settings, mail accounts, etc.
Secondly, I have a separate backup for all of my jailbreak apps, tweaks, and settings. For this, I use PKGBackup.
I've found that the combination of the iTunes backup coupled with PKGBackup makes for a quick, and painless restore back to my favorite settings.
There's one problem with this methodology though; it doesn't backup all of my SMS messages...