OS X 10.7.5 Applications folder nearly empty; documents gone from Word

Suddenly my Applications folder was absent from the dock (I put it back). But now it's nearly empty! I can see my apps in Finder. Also, tons of my documents are no longer in Word--templates of our letterhead, papers...just gone. I've been messing around b/c my hard drive space was full, but I didn't think I did anything that important. Help, please!