I upgraded to El Capitan and since then i haven't been able to compile. I found som helt that MacTex have been moved from /usr/texbin to /Library/TeX/texbin/ and changed the paths. I can now compile some of my Tex documents while others makes my computer go into some infinity-loop and overheating...
Differences between the documents i can and can't compile seems to be either if they contain TiKZ or Biblatex? but i'm not sure.
Here is a picture of my setting i TeXmaker:
:)
Could you provide a sample document in which the computer crashes? Sometimes, a small typo in a TikZ document can propagate some odd behaviours. So far, I've got no problems with El Capitan.