DJ,
As a (primarily) nature photographer the tele's are something I've researched quite a bit.
I use many Contax lenses on a 5D as well as S2b/Aria, including amongst others the 21mm f2.8, 28mm f2, 85mm f1.2 and 135mm f2; but Canon prime tele's are pretty hard to beat (especially on a Canon body!).
I have the 300mm f2.8L IS, and it is a phenominal lens, really quite extraordinary performance and image quality, as is the 600mm f4L IS.
But both were very expensive, and if you're looking for a less financially crippling option, then Canon's 300mm f4 and 400mm f5.6 primes both get very good reports, and I have seen many wildlife photos taken with these lenses that looked pretty damn good to me.
The 100-400mm gets mixed reports, which in my (costly) experience of Canon lenses means that it's a mediocre "consumer grade" lens, raved about by people who've never seen what a really great lens can do.
I believe the 300mm f4 now comes in an IS version, and one cannot appreciate the benefits of IS in a tele' until experienced. It is such a huge advantage that any competition would have to be staggeringly good to better it.
As an indication, I had a copy of the famed Contax 300mm f2.8 (I believe it retailed at GBP13,000 when new) to test against the Canon for a few days earlier this year. As beautiful as it was, and as much as I love the Zeiss look, the Contax did not win that battle.
You can also use a 1.4x extender on the Canon tele's with pretty much no discernable loss of quality.