So a normally simple upgrade from standard 2005 sp3 to 2008 was a little but of a pita. Backed up all the dbs, including system dbs. Then go through the upgrade steps. It failed with an error about not being able to find sqlncli_x64.msi. Try a repair on sql native client, and fire up upgrade again. Same error.
Uninstall sql native client, try upgrade again. Failed for an error about a service stop or start not responding. I couldn’t manually start sql agent. So I extracted the sp3 files using the -x flag and reinstalled sql native client. Agent started, but the upgrade failed again. Check the “add/remove” programs again carefully and find sql 2008 native client also installed from about a year ago. I uninstalled that and ran the upgrade again, and success!