Oddly enough I’ve been on a bit of a crossover fanfic binge recently. Obviously this is an area where personal mileage varies (a lot) but I have to say that some of the shipping that goes on makes me go "ewwww". I’ve seen enough of this recently to have a personal rule: stop reading as soon as it goes beyond the ratings level of any contributing universe.
Another problem for me with shipping is that the fandoms I might be interested in reading about usually have well visualised relationships that are firmly grounded in the characters. So messing with those relationships tends to trigger a "No, no, no! X would never do that! And Y would run away!" reaction. This tends to kill my interest in that story stone cold dead.
I did run across a fabulous, if regrettably unfinished, BtVS/Firefly crossover that made better use of Xander than much of the original material did. It didn’t seem to be shipping Xander with anyone though.