I've been reading this forum for quite some time, and I just recently tested these lenses. Since people ask about both of them, and about comparisons between two of them in particular, I thought others might find my test useful. I approached my test from what seems a ->radically<- different perspective as most of what I see in here, backwards even, so let's talk about my methodology first, then why I selected this type of test:

First, I selected two test subjects: a smallish doll or "action figure," and a large and somewhat ugly Indian statue. This tests near and far focus capabilities for each lens. The 100~400L was tested against the 400L at 400 mm, and against the 300L at 300 mm. For each subject for each lens, I shot 20 exposures at f/5.6 and another 20 at f/8; half of these were focused manually though an Angle Finder C, and half using autofocus. I picked the best image from each lens+aperture combination. I then made 11x14 inch prints from the best image each lens had given me at each aperture. Finally, I gave these prints to my good friend who teaches a community college level photography class. He passed them out among his students and asked them to choose the best print for each comparison. The prints were randomly marked with "A" and "B" to allow statistics to be calculated later.

Why: I've seen more message postings and links than I can count, showing the measured resolution of these lenses in different circumstances, and leaving it up to the viewer to determine whether any difference is meaningful. I approached this test from another angle: I tested whether any of these lenses are noticably better than others, and leave it to others to determine exactly how much difference is there.

Now for my findings.

400 mm f/5.6:
* 27 students chose the 400L
* 1 student chose the 100~400L
* 1 student was undecided

400 mm f/8:
* 22 students chose the 400L
* 3 students chose the 100~400L
* 4 students were undecided

300 mm f/5.6:
* 28 students chose the 300L
* 1 student was undecided

300 mm f/8:
* 19 students chose the 300L
* 4 students chose the 100~400L
* 6 students were undecided

I'm a little surprised at the results. I expected to see a difference in favor of the prime lenses, but I didn't expect the difference to be this pronounced. Looking at the prints I agree with the results. The differences are noticable, but not glaringly obviuos. Please remember we're discussing an 11x14 viewed by photography students.
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Have fun!