When I upgraded to 3124 (OSX El Capitan), I noticed that I didn’t have Package Control installed anymore (the command palette didn’t have Package Control items). The release notes for 3124 mentioned that SublimeText baked in a way to install Package Control, so I looked for that option in the command palette and couldn’t find it.
It seems that, for some reason, Package Control was added to my ignored_packages array in my preferences. I’m not really sure why, but removing package control from the ignore packaged list brought everything back to normal for me.