The IS on the 300 F4L is useful for wildlife/birds that don't move much or too dramatically. I've gotten very nice shots in low light of herons, ducks, geese, cormorants, etc that are not feasible with the 400 f/5.6L. You could also get nice shots of turtles, rabbits, squirrels, and similar.
As m_r noted, the biggest difference you will see is in the AF speed with the 1.4x TC - the quality is still quite good, though it improves if you stop down a bit.
If your primary area of interest is smaller birds or birds in flight, the 400 5.6L is the lens to get - it's probably the best birds in flight lens in the world, from any manufacturer.