My earlier comment notwithstanding, I think I've figured out what's going on. The issue seems to be Package Control, most likely the new version update to 2.0. I just restarted ST2 after having it open for the past few days, and happened to have the console ( Ctrl ` ) open, and saw that several of my packages, including Tag, Terminal, and SublimeREPL, were added to the ignored packages list. This typically happens when a package is being updated or removed, and is done so it can't be used halfway through the operation before everything is synced. At any rate, for me there was some sort of error, and I had to force quit Sublime and restart it. I immediately checked my preferences, and sure enough several packages were in the "ignored_packages" array.

So, I'm guessing something like this happened to you, and for whatever reason the packages weren't removed from the ignored list, possibly because the system update didn't complete normally. Hopefully this won't happen again, but if it does you'll know where to look. Additionally, if it does happen again, I'd submit an issue on Github, as this may be a bug.

Update