After upgrading to iPhone SDK 3.0 beta3, I found all my Xcode projects only had two build options remaining: iPhone OS 3 Device and iPhone OS 3 Simulator.

I still need to build for multiple systems to test all the custom iPhone development we do at Surgeworks, but I also need iPhone OS 3.0 so I can diagnose issues and get all our Native Apps ready for the scheduled release of new iPhone models in June that will feature the new operating system.

Ivan Kalaica suggested how to fix this issue: to check out all projects again from SVN (Subversion). That worked, and all targets are now available in Xcode again.