So when I'm ready to install a new ROM that requires a wipe, before I do anything, I do a nandroid backup just in case anything goes wrong.
Then I'll open up Titanium Backup, hit the menu key, then batch. I'll scroll down to the bottom and delete all my old backups (I like to start fresh). When they're all done deleting, I'll run Titanium Backup again, hit the menu key, then batch. Then I'll backup all apps and data and let that run until it's complete.
Now I'll load up my ROM. Since I go back and forth between regular AOSP-like blurless ROMs quite a bit , my restore process may be a little bit different. When my new ROM is loaded I download Titanium Backup from the market and run it, hit the menu key, then batch. Then I'll go to restore all missing apps and data but not just automatically hit run. I go through all the checkmarks and make sure it's not installing anything from the old ROM that I may not want on this one so I usually have to uncheck a few boxes. I just let it restore my downloaded market apps and data, NOT system apps.
Hope that helps.