Some would argue that a protein skimmer should be put before a refugium as to not skim out any copepods, eggs, or anything produced within the refugium as food for your fish and corals...
Me personally, I don't think it really matters unless you have a huge skimmer with a huge pump that processes a lot of water. For the regular home aquarist, however, a skimmer before a fuge makes the most sense.
It makes sense because you can also include your skimmer in the overflow section of the sump - and keep all the bubbles contained in one section.