Jeanette posted some excellent photos of some Ibis in flight just recently, using a non-L Canon lens and in my book, they were very good indeed for a very challenging subject.
I have enjoyed some success previously with our older Pentax *ist DS and the 55-200mm kit lens, although the success rate was well down compared to our new set up.
A telephoto lens of 200mm plus is almost essential for bird in flight photos, but where the L lenses seem to give a distinct advantage is, as Alex mentioned, their quality when wide open and the resulting speed of auto focus.
I also think that flying birds find the off-white L lenses very attractive and so try to fly down the barrel so to speak, another L lens advantage!
Cheers
Dennis