I did the 300 f4 IS vs. 400 f5.6 thing a while ago. I went for the 300.
The clincher was IS. I know that it doesn't help with moving subjects or on a tripod and all that jazz but it really does help when hand-holding. Given that cameras these days have such cramped sensors, anything that helps reduce blur from shaky hands is a no-brainer.
Also, having a 300mm and effective 420mm lens is pretty useful. You aren't losing any light over the 400mm 5.6.
Here is the catch:
At least with my copy, I find that the 300 doesn't get really sharp until it is stopped down quite a bit (like 7.1 or 8). Add the 1.4 extender and you are into a pretty slow/dark zone. I don't know how sharp the 400 is wide open (never used one myself) but that might be a consideration.
If you are considering the 300 f4.0 non-IS then I'd skip it and get the 400.