I have had no issues with my phone since the Gingerbread release, and the small maintenance release I got today.
Prior to the GB update I had rooted my phone. When GB wouldn't load on a rooted phone, I reloaded my saved ROM, installed GB and away I went. All downloaded apps work.
For those having issues with trying to get the update, keep pressing the HTC software update option. I had to do this twice today to get the maintenance upgrade and at least three times before the GB upgrade would initialize.