I still haven't figured out how to back up my e-mails
and preferences from MAIL.
Anybody?
In your home folder, go into the "Library" folder.
Save the "Mail" folder from it, as well as any "Mail" folder inside "Caches" (make sure you know which is which, and put each back into it's proper place, probably overwriting like-named folders in the new system.) and also the com.apple.mail.plist file in the "Preferences" folder.
Note: the Caches and Preferences folders I'm referring to are also inside the Library folder.
As for the iTunes and iPhoto folders, it's actually easiest to run Software Update before wiping the old system to make sure you have the latest versions of those that'll be updated to on the new system, and then save the entire "iTunes" folder from the music folder and "iPhoto" folder from the pictures folder.
Also, any plist files and Caches folders for any apps you use from Safari to QuickTime will help you keep stuff you might otherwise lose.
As for me, I mantain a backup clone of my hard drive on a firewire drive and after a restore keep it old for a day or two to make sure I've copied over everything I want or need. As being human, I'll generally forget something at the time and have lost a lot of goodies that way.
Good luck.