I also have suffered from this problem which began with the 10.6.3 update. I have a 20" early 2008 iMac w/ the ATI Radeon HD 2600 PRO.
There is a fix that has worked for me every time there has been a Mac OS X update--re-installing the
10.6.2 kexts. I had to reapply them again after the most recent update, but it solved the problem as usual. I've been reapplying the kexts for every update since at least 10.6.4, and I am running the latest version of Lion with the old 10.6.2 kexts applied and it has been stable.
Here is the huge thread on apple.com that discusses the issue - I'm linking to the page that has the solution from KrzysiuTurek (scroll down to see his 1/10/11 post)
https://discussions.apple.com/thread/2384136?threadID=2384136&start=300&tstart=0
I believe there were refinements/more detail to his suggestions later in the thread but since it is 73 pages long at the moment I can't easily find it without reading the whole thread, but before trying this solution,
make sure you have a good backup and I would advise reading the whole thread (at least from the point linked to above) to make sure you understand the risks and know what you're doing and to be sure you get the right kexts for your machine.
Good luck! I hope it works for others. It worked for me. FYI: occasionally when I run Kext Helper to do the fix, it will apply the kexts and give me the message that everything looks good, cross your fingers and reboot, then Kext Helper becomes unresponsive and crashes, but on reboot everything works fine.
I have reported the freezes to Apple on several occasions, as have many in the thread I linked to, but so far the issue has never been fixed. It's very frustrating, but at least there is a workaround.