Letting Apple control most facets of your computing experience is just a fact of life for the Mac faithful, but if you want to swap out the hard drive for a bigger or faster one with the most recent iMac refresh, well, you have somewhat limited options. Rather than a 4-wire SATA configuration Apple uses a 7-wire configuration that keeps you from hooking up just any old hard drive, lest a temperature sensor go batty and your system refuse to cooperate. There are ways around it, but your warranty may not apply afterward...
Update: We've revised this post to clarify that this isn't exactly a new issue. The same problem existed in previous revisions, but the big issue now is that the separate thermal cable has been integrated into the SATA cable. It's similar to what was done before, just a little harder to get around now. But, you can get around it.
Update 2: Hardmac has a detailed analysis of the situation which we'd recommend you check out. It verifies OWC's findings, and recommends you short pins 2 and 7 to basically circumvent the issue. Why does Apple do this? The separate temperature monitor enables OS X to more regularly check the temperature of the system's drives without compromising overall bandwidth provided by SATA.
[Thanks to everyone who sent this in]