I recently moved from a 40D to a 1D2 when I found a great local deal on a 1D2 with only 1300 actuations. I've read a lot of forums comparing these two, but thought I'd contribute my thoughts on the switchover after spending a week actively using the two bodies side-by-side with the same two lenses, the 35L and 400 5.6L. My main interest is in wildlife photography, especially birds and (more especially) birds in flight.
The differences between the two cameras have been well-noted, so there's no need to re-cover all that ground. I, for one, won't miss the 40D's sensor cleaning, built-in flash, full-auto modes or smaller weight/size. (The last item may be a big factor for some; compared to the 40D, the 1D2 is a big old brick---you're going to notice a difference when carrying it around all day!)
I do find myself missing the larger crop factor. The 1D2 is 1.3x versus the 40D's 1.6x. While on both cameras the 35L can function as an amazing "standard" lens in the vicinity of 50mm, the crop difference is quite pronounced on the 400L, where the net loss in focal length is over 100mm! (From 640 to 520.) One could argue that the shorter focal length makes the 400L easier to handhold, but once I learned to keep the shutter about 1/1250, I never had a problem handholding at 640. This loss in reach---coupled with a loss in megapixels, since the 40D is 10mp and 1D2 is 8mp, means that your faraway subject appears to be quite noticeably smaller on the screen! For what I do, it's the single most dramatic negative difference in moving from the 40D to the 1D2. (I suppose one could overcompensate for this by getting a 1.4x TC.)
The 1D2's small and relatively low-grade LCD screen is another tradeoff---it makes it difficult to tell whether you've got a sharp picture or not until you get home and view it on the PC. Really, the LCD is pretty awful. However, for most bird-in-flight shots, time is of the essence---you either got the shot or you didn't, so there's not much sense in worrying over the image in the field on the LCD.
Really, the only other negative is the shift from the 40D's super-intuitive and easy-to-navigate menu system to the 1D2's considerably more involved interface. As has been widely noted, the 1D2 was designed to prevent the accidental changing of settings, and this was accomplished by making many functions dependent upon the pressing of two buttons rather than only one. This includes not only changing ISO, etc, but also playback features like scrolling through your images or zooming into them. If, like me, you absolutely loved the 40D's user interface, you might find the 1D2 painful at first, but after a day of playing with it (and studying the manual---a must!), I found it manageable, and a week later it's become just as natural as that of the 40D---even if at times it still seems needlessly cumbersome. To be clear, on the 1D2, you do NOT need to press two buttons in order to change aperture or shutter speed---those you can easily change with the camera held to your eye.
That's about it for the negatives. Now for the positives.
Again, a lot of this ground has been covered already---the 1D2's big viewfinder will blow you away after using the 40D. Just the feel of the camera in your hands will probably make you grin foolishly. The many many many customizable features (overwhelming at first, then totally liberating) are great. Read a bit in the forums and you'll get your head around some of these.
The most important thing to note---since this switch does involve a hit to crop factor and megapixelage---is that, after dozens of side-by-side comparisons in which I used both bodies tuned to identical settings (ISO, speed, aperture, metering, etc) using the same lenses, the image quality of the 1D2 is at a minimum equal to (meaning never worse than) and in the vast majority of cases noticeably superior to that of the 40D. Yes the picture will appear a bit smaller on the screen, but it's also sharper and brighter, and there's something indescribably better about it, too. (If I could explain it, I would.) Megapixels aren't everything---the 1D2's sensor is simply a better sensor---the 40D is crowding all those MPs onto a smaller surface and while it produces wonderful images (don't get me wrong---the 40D is an awesome DSLR!!!), it's not quite 1-series quality. I had my wife take a blind comparison test between the images and in every single case she picked the 1D2 image as better. (Even in those few cases where I cropped and resized the 40D images to make them nearly identical in size to the 1D2 pics.) So don't believe the hype about MPs! The difference between 10 and 8 is very slight anyway, and this 8 way outperforms most 10s. Unless you're planning to make huge prints (meant to be viewed from a distance), the 1D2 is the better choice.
The next big thing---and maybe just as important as IQ for what I do---is the autofocus system. Simply put, there's no real comparison here. The 1D2 has 45 active autofocus points and its ability to track a bird moving erratically through the sky is going to amaze you if you're used to the 40D. The 40D isn't bad for birds in flight, but my keeper rate was pretty low on that body. On the 1D2, my keeper rate---even my first time out when my subject wasn't even a bird but a tiny dragonfly!---was close to 100%. And on the 1D2 you get a lot more control over the AF system than you do on the 40D. You can adjust how many AF points to use, how sensitive you want the tracking to be, etc. Once you sort out what settings are best for you, you'll find that this camera keeps your subject in focus even as it moves behind and in front of trees and other obstacles. The AF is what sold me on the 1D2. The ability to link the metering point to the active AF point is nice, too.
I find that the weight of the 1D2 is not a burden but actually a boon, as it better balances the weight of the 400L. That said, you'll want to invest in a good padded strap for such a rig!
There's a lot more to be said (and it's all been said elsewhere). The battery-life on the 1D2 isn't quite as good as that of the 40D, though after a week of fairly frequent use, I'm still showing a good charge. The ability to record onto two memory cards (one CF and one SD) on the 1D2 is great. Some use this feature for backup, recording the same file simultaneously on both cards. I intend to use this as storage expansion, with my 8gb CF and my 4gb SD.
All in all, I'd say that for someone looking for a birding camera, the extra $200 or so needed for the 1D2 (over the cost of the 40D) is worth it.
NOTE: the two sample images are 100% crops, the first from the 40D the second from the 1D2. Both were with the 400L taken in stable conditions about 15 seconds apart from each other (just enough time to swap bodies!). Both were shot at ISO 125, 1/1000 sec, f/5.6, using spot metering. The pictures give some idea of the difference in scale between the 1.6x and 1.3x crop and 10mp vs 8mp, but more importantly showcase the difference in IQ.