Haven't read either Girl Genius or Schlock Mercenary. The others are regular or semi-regular reading.
The only other webcomics I follow that might have a reasonable basis for a crossover are Tweep and Marry Me (Anders Loves Maria has already been done, and delightfully), which could definitely work (as long as we give Mr. Crosby a decade or so to get around to it. I'm not complaining, just observing). I'm sure no one on staff at CoD would admit to rocking out to Stasia's pop now that Raven's gone.
Red String* might work save for the location problems and perhaps age differences, but somehow Johnny Saturn, Flipside, Zona, The Meek, Goblins and Locus don't seem like crossover fodder (of course, neither does OOTS, save that anything seems to be able to happen there).
*Stop judging me!