The
EF 400/5.6L USM is preferred by "bird in flight" photographers because of the fast AF and long focal length. Since fast shutter speeds are needed to freeze the wings anyway, the lack of IS isn't a big deal.
Personally I prefer the
EF 300/4L IS USMfor general wildlife work, since you can always add a 1.4x TC and get a very good quality 420/5.6. AF with the TC is somewhat slower than the 400/5.6L, but it's still fast enough for most subjects. The faster aperture of the 300/4L IS is useful too when working without a TC and of course the IS can be very useful indeed if you're working without a tripod.
If I could have just one (relatively) inexpensive telephoto prime for general wildlife work, I guess it would be the 300/4L IS USM, though I'd certainly also consider the
EF100-400/4.5-5.6IS USM too if the slightly higher price wasn't an issue.
See my review of the
EF 100-400IS for some comments on a comparison with the EF 300/4L