As far as Nikon mounts... (Cannon should be a similar story.)
I tried the 80-400 VR (f/4.5-5.6) about a year ago when I was shopping for the 70-200 VR (f/2.8). I guess it depends on what you need. If you need something slow, with better reach, the 80-400 would work fine. But it focuses slow, dosn't have a constant aperture, and telescopes in/out which means it's going to be sucking dust and dirt into the inner glass. The 70-200 on the other hand, focuses lighting fast, has a wonderful fast constant aperture, and dosn't telescope in and out so it's completely sealed. Plus, if I need to go out to 400mm, I can slap a 2x converter on, and have the same f/5.6 that the 80-400 has at 400mm.
I would assume the same can be applied to the Cannon IS lenses... sealed, constant ap. lense that focuses lighting fast, or a non-sealed telescoping lense that focuses a little slower, but has more reach.