When I upgraded from the OG Droid to the Droid 3, I took no steps in backing up apps. After activating the Droid 3, I found that 100% of the 'purchased' apps from the App Market were automatically downloaded and installed. Just a handful of the 'free' apps that were installed on my OG Droid were automatically installed. In fact, many were no longer listed under 'My Apps'.
None of the apps from the Amazon AppStore automatically installed, however, the ApStore had a complete list of the apps I had obtained from there.
I still have my OG Droid, so I can see the apps that I installed.
Not automatically installing apps from either the App Market or the AppStore is an inconvenience.
However, since the Droid 3 is more powerful and has more storage, I used this as an opportunity to test some different apps as replacement for those app that were not automatically installed. I spent a good portion of one evening while watching TV to test apps and install what I wanted. In some cases, I used the exact same app on the Droid 3 as on the OG Droid and in others, I used apps from different developers.
Good Luck,
Bob