I got fallout3.iso using DC++ at university, some other student had it so I downloaded it from his computer. My computers graphics were nowhere near good enough to run it so of course i deleted it, also from the recycle bin. Ever since then, the hard disk space on my computer just kept disappearing.
I used 'moleskinsoft Directory size' to locate where all the missing disk space was going to, and it was in the $Recycle folder. From 3gb, Fallout3.iso all of a sudden was 66.6gb. So I simply deleted it with moleskinsoft.
Now my computer is running perfectly fine, with nothing disappearing on me.