I think it is finished, well sometime on Saturday it finished. It would have been nice if there was some indication of progress during the upgrade. The black screen eventually went away and I could log in from the console. For a while things stopped working, but that was because the upgrade activated the Windows Firewall which I had turned off.
While it was on the black screen I could remote desktop in, do somethings, but not start stopped services unless they started on boot. At some point it activated the FW cutting off remote desktop and some things I was using, but not SQL server or IIS they survived the FW activation. Possibly their installation automatically put in the correct FW rules.
Overall the upgrade went ok, but it took a really long time. If I had the HW to spare I think it would have been better to install from scratch.
I am leaning to not finished yet. The upgrade really needs some kind of progress bar.
Things are looking ok if a bit strange, and I am unsure if the upgrade is actually complete. The strangeness is that the local console has a blank screen with only a mouse cursor, but I can remote desktop in without any problems. The machine is running at 100% CPU so something might not be finished.
Things to note when doing an upgrade from Windows 2003 to 2008. Run adprep before starting. adprep can be found on the 2008 disc. You may also need to set your Domain to be 2003 native. It seems that by default it is set to 2000 mixed. It can be changed via the AD domains and trusts program. Also make sure all the remote desktop sessions are shut down, you will not be allowed to upgrade if there are multiple people logged in.
Things that are now working yet, Apache which I use for SVN, is not starting up.
Things that are working, SQL 2005, my blog, and my site that prompted the upgrade. Once it is finished enough for the public I will publish the url, for now it is private.