Its interesting that Yamaha does not mention using a water seperating fuel filter like the Racor on their waverunners, when they are adament about you using one with their outboards. The 4 strokes do have a water separator, but I've never seen water in mine, so I wonder how well it actually works.
Good question, especially with ethanol fuels becoming more and more standard, but I personally don't know of anyone using an aftermarket filter on their ski.