I think 400mm is the best all around focal length, but it's hard to get to that length in Canon affordably. I like the 400mm f5.6 but it does not have IS and is a bit slow at f5.6. I won't buy a lens without IS so that one is out for me.
Your next option is the 300mm f4 IS and you can pair that with a 1.4x. It's a good combo but one thing I notice about this lens is the IS is fairly outdated. The new IS is night and day different, although it has it so it's a decent option. Although it's a bit short, with the 1.4x it can be managed.
The last option is the 100-400mm f5.6 IS. I can't find a sharp copy of this lens. Many swear they have sharp ones but I've never seen one. It really isnt a 400mm either, it tops out at 380mm and the last 50mm on the top end are the worst quality of the whole focal range. I just can't like this lens no matter how hard I've tried. It also has the old IS system that the 300mm f4 does.
Those are your 3 best options for about $1000. One nice thing is that if you buy one of these you can sell them for 80-90% of what you bought them for when it's time to trade up. I would venture the next step up is the unbelievable 300mm f2.8 IS. From there you can keep that with a 1.4x or step up to the 400mm f4 DO when you get a few extra bucks. If you don't leave the road often the next logical step may be the 500mm f4 IS. Give me a 400mm F4 DO and I'm happy if you can find a nice sharp copy. The 400mm F4 DO is the only lens I use that makes the Nikon guys have lens envy...