Presta valves are slimmer, and so the smaller hole for them has less of an impact on the strength of the rim. You can also use slimmer rims than with schraeder valves. I think they can also hold a higher pressure without leaking as much as schraeder valves too.
Schraeder valves have the advantage that they are the standard for cars and most bikes, so you're more likely to be able to find a pump to fit, although lots of pumps are adaptable.
I prefer schraeder, mainly cause I seem to have a habit of snapping prestas, and the impact on rim strength and leakage are so slight they're pretty much unnoticeable.