Apple does a good job of keeping backups of your iPhone data, but they don't backup everything. Here's a list of stuff you have to fix after you reflash your iPhone:
- Passcode Lock: Settings - General - Auto-Lock, Passcode Lock
- E-mail: If you leave mail on the server, your iPhone will forget which e-mails you have already read, so you'll have to read or delete them. A couple of tricks:
- Reduce the number of messages displayed in your inbox - Settings - Mail... - Show
- In Mail, hit "Edit", then select a bunch of messages and delete them all at once
I'll keep adding to this list as I remember stuff.