Dork. they're only part of the puzzle. Personally I think they should be used for conditioning more than muscular endurance. before I get started I should say these two terms are not mutually exclusive.
Let me clarify how I beleive on difers from the other. Muscular endurance is being able to do 200 pushups. That's quite a few and nobody here will doubt that that's pretty good endurance. Conditioning I would say places more emphasis on cardiovascular work. So doing tabata intervals, 3 minute rounds or circuits, or something like that is for conditioning. what really separates the two is time. The guy doing 200 pushups can sort of rest in the up position, but make him do those pushups in three minutes and he's gonna be breathing HARD at the end. This is how I beleive bodyweight exercises should be used: with temporal goals or limitations.
In fact, if you go to my website, you will find my little program randomly generates bodyweight GPP drills that work much like that. this is the kind of muscular endurance you want in sport, you want to be able to push as hard as you can for an interval, rest a bit and repeat.
To be honest, for most athletes I'm not sure what the advantage of posessing just straight muscular endurance would be.