I know this isn't a CF/SD card thread, but I thought I'd toss in one other thought which is completely independent of the camera being used: the speed at which you can trasfer images off of the card is different between those two types. That likely doesn't really mean anything to most of us, but to some people that shoot a lot in the field and need to empty a card quickly to get it back in the camera, it may matter. Otherwise, its moot.
I went from a 40D to a 5D and then a 5D2. It's hard to describe the difference until you've experienced it, but there definitely is one. The move from 1.6X to FF takes a little bit of getting used to. As stated previously, lenses are different at full frame. You're using corners of lenses that you haven't used before on crop bodies, so one with corner softness becomes more pronounced. I noticed a difference in the AF systems between the 40D and FF models. The obvious things are noise levels, etc are much improved.