The option "Data Files" is greyed out. I've tried running the launcher in administrator mode and it won't let me either (was my only guess). So I can't activate any mods. Why is it greyed out and how can I fix it?

This happened to me as well once. Can't remember what really caused it, I believe it was some mod or whatever that I had installed. It was something that I installed for Skyrim at least, that's for sure. After uninstalling it, or reinstalling Skyrim(I can't remember which) it worked again. It might have been something related to the Workshop, again, I'm not sure. I just recall having the same issue and somehow fixing it by uninstalling something. Not much for help, though.

Just a thought...if you've got Steam offline, try putting it online. Maybe it's partway through downloading something?

So have you already gone through the bdatafilesenabled=1 (something like that) process in the prefs.ini?

I'm not sure what that means.

I'm running steam in online mode, I've only installed 6 or so popular mods. I' can't recall ever having access to the Data Files button, so if I uninstall anything it would have to be skyrim, but then wouldn't I lose my saved games?

http://i.imgur.com/1u68e.png

"Finished synchronizing subscribed mods!"

... that's nice...

Is that a workshop thing?

Yeah, that's steam, it runs through all the mods and updates them.

I didn't remember the command name correctly. :/ Go to C:\Users\Username here\Documents\My Games\Skyrim or the equivalent path and go into the Skyrim prefs file. Go to "Launcher" and below it enter: bEnableFileSelection=1
If you haven't done so already.

Ah, thanks everyone, I reinstalled (skyrim) and now it works.