the-digital-picture.com discusses this in many of his reviews.
From what I understand, The best 400mm IQ and AF performance comes from the 400mm f/5.6 L (assuming we are only talking about lenses in this price range). But you don't need 400mm very often so it would be kind of silly to buy a 400mm prime. The 100-400 comes next followed by the 300 f/4L IS +1.4x tc. The 300 is faster and has better IQ at 300mm, but sgain, since you don't need the longer reach very often, the zoom makes more since.
I think Sigma used to make a 100-300 f/4 that is supposed to have pretty good IQ. If you paired that with a tc you could get to 400mm and retain AF (I think). This might be a more affordable alternative to the 100-400.
Having said all of that, the 100-400 seems like your best bet. I was in love with this lens for awhile and then fell out, kind of waited for its replacement, and am staring to lust for it again. They pop up here used pretty frequently. Buy one, try it, and if you don't like it, sell it.