I own the 5D and the 40D. I am an amateur, not an experienced pro like Michael.
If I did not have either camera today, based on my experience, if I had to buy today, I would buy the 40D. Let me explain why. First, see Michael's watch parable.
Unbelievable as it sounds with its smaller pixel size, the 40D has a cleaner, high ISO image, which is also cleaner in the shadows. It seems to have a very accurate and quick autofocus and better automatic white balance. It is slightly smaller. Its unsharpened images seem a bit softer than the 5Ds, but I am not using my normal RAW processor (Lightroom or ACR).
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There seem to be a lot of conflicting reports on the 40D versus the 5D. For example, Bob Atkins is a very experienced photographer with a greater knowledge of technical matters than most and his review of the 40D places noise at slightly worse than the 20D, with the 40D's noise reduction off, and slightly better than the 20D with the 40D's noise reduction on. The significance here is that the 40D's noise reduction does not appear to reduce resolution, so there would seem to be no reason not to use it.
However, when comparing noise from cameras with a different pixel count, one has to be careful one is comparing
equal size images, which means either the 40D image should be interpolated (together with the noise) to the 5D size, or the 5D should be reduced (together with the noise) to the 40D size.
Having done this, I would expect, judging from the reports I've seen so far, that any noise advantage of the 40D over the 5D (if it exists) would be too marginal to be of significance.
The real reason for choosing a 40D over a 5D would be the benefits of the cropped format in conjunction with a higher pixel density, which offers greater telephoto reach, and such factors as more accurate and faster focussing, live preview and so on and particularly the cheaper cost, not only of camera body but of telephoto lenses.
The downside is wide angle performance. Where are the 10-22mm (EF-S) lenses that are of equal quality to the Sigma 15-30 or Canon 16-35?
Maybe I was unlucky with my purchase of the Canon 10-22mm. After trying a different copy of this lens in three different countries, I found one that was nearly as sharp as my Sigma 15-30.
However, having compared equal FoV shots from my 20D plus 10-22mm lens with 5D and Sigma 15-30mm lens, it's clear to me that the superiority of the 5D image is more than pixel-peeping small. Since I use the Sigma 15-30 a lot for landscapes, I can't see a 40D being a complete replacement for my 5D.
I also get the impression that the 40D's resolution is only very marginally better than the 20D, as one would expect with 10mp versus 8mp.