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This is a question that's been asked quite a few times and there's already been a fair amount of discussion.
I own both and find it very difficult to choose between them - they'e both Canon 'L' series lenses so the optics are superb.
As to which lens I take out with me then it's a question of what I expect to be doing.
Purely for bird photos then I prefer the 400mm f5,6 as it's a little lighter and more compact and works well with teleconverter attached. I also prefer the built in lens hood. The autofocus is slightly faster as well, so better suited for birds in flight.
If the weather isn't so good with overcast skies the I prefer the 100-400mm as the IS helps a lot when hand holding. I also find it's a better lens for close up (macro) photos with extension tubes attached as it has a lot closer minimum focus. Even without the extension tubes the closer minimum focus maks it a better lens for feeding station use where birds are petty close. It takes a teleconverter as well but how effective it is in operating seems to depend on the camera body good with 30D - okay with 20D - less okay with 400D and 350D.
If you look in the Canon forum you'll locate the other threads where these lenses have been discussed at length. The zoom was once regarded as inferior to the prime by some, but many regard them as equals now.
