So I decided to load latest Bugless Beast to check it out, and like a lot of people out there not looking forward to installing all of my apps again. But there I was after the nandroid restore, looking at an blank homepage and empty drawer.
Then an idea hit me. I did a factory data reset on the phone, with the purpose of getting back to the initial Google log in screen. Entered my information, and it began the sync.
If you do this, LET IT SIT! It's doing it's thing. Let it sit even after the sync icon goes away, as long as the 3G is still showing data transfer, TRY NOT TO MESS WITH IT. DO NOT OPEN MARKET, as I think think this interrupts the app restore and you have to do the rest manually. Check your drawer from time to time if you must, you will see your apps coming back. After it finished, I got a notification icon saying "38 Applications Restored." Even got my wallpaper back. Many ROMs will allow you to keep your data, but if you are going between major revisions (like 2.0.1 to 2.1) it works like a charm.
Edit: ALL of my applications that were listed in the "Downloads" section of the market prior to the install came back.