UPDATE: This has nothing to do with the security update. It is related to Audio Output Settings!
Security Update 2006-002 (Intel) Some misbehaving application apparently has broken the audio in most of my SDL applications as well as QuickTime muxed MPEG-1 and MPEG-2 audio in my mpeg files.
I found that Tux Paint still had audio. Armed with this knowledge, I removed the SDL Frameworks from my broken applications (Blob Wars and SuperTux) and installed the latest SDL frameworks from http://www.libsdl.org into my /Library/Frameworks directory. Happily, both games have sound again.
Lbreakout2, on the other hand, looks for libraries rather than frameworks. I made symbolic links to the actual libraries in the frameworks but lbraekout2 complains about incorrect library versions. I am trying to compile it from source but it dies claiming not to be able to find libintl.h!
I have yet to figure out why my mpeg audio no longer works.