If you want to use a 27" iMac's screen and a 24" Cinema Display as one desktop, the physical size differences will forever keep annoying you (as will the differences in style/physical appearance/design). They will never disappear. Therefore I would go for 2 identical screens, and I'd have sales people, in the store demonstrate to me which iMac, MBP, or MacPro supports 2x 24" Cinema Displays. Or even 2x 30" Cinema Displays! Might as well go the distance while you're at it! That's the Mac, and the displays, that I'd get.
I have a 17" MBP, and a 20" and a 24" iMac. I work on a friend's 30" Cinema Display (off my MBP) often. He's got 2x 30" Cinema Displays (and 2x MacPros; he's got an audio recording studio), but I work on only one of those 30-inchers, because two feels simply uncomfortably big for me (doing photo editing and management) as a work area. Running presentations on the two lined up side-by-side, though, is breathtakingly brilliant and impressive!