[Cairenn]

Do you use cosmos? Their patcher will delete anything and everything it doesn't recognize as being a part of itself (aka all the rest of your mods) if you have the "keep directory clean" option enabled. To prevent it from happening again in the future, you can do one of two things. Either:

a) turn off the "keep directory clean" option; or
b) add a .nopatch folder for every single one of the other addons.

If you want to keep using the "keep directory clean" option of the cosmos patcher, you should make a backup copy of the other addons, which you copy into the wow\interface\addons folder after you finish running the cosmos patcher, every time.

There was an extensive thread on this topic in the Blizz forums, but it seems to have dropped off now (can't find it any more).

If you aren't using Cosmos, I've no idea what else could cause this to happen.

(edited for clarity)