My experience...
I just wanted to pitch in that I also had the same extremely frustrating problem with a two-month-old 2.53 Macbook Pro that had been updated from Leopard 10.5 to Snow Leopard 10.6: long spinning beachball blocks on the order of 5-60+ seconds without any significant CPU activity. This was frustrating since there didn't seem to be any pattern to which applications were open--Terminal, Mail, Firefox, Safari, iTunes, didn't matter.
It did appear as if putting the system to sleep and then waking it again aggravated the frequency of blocks, but I have no real evidence of this.
I installed the recent Snow Leopard performance update 1.0 from Apple to no effect.
I tried the recommendations of several forum users:
- Uninstalled the Adobe Flash player
- Ran the Snow Leopard Cache Cleaner's scripts
- Turned off secure virtual memory
After a restart, the system appeared stable, but after a quick stress test -- opening a number of applications (MATLAB, Pages, XCode, Numbers, iTunes, Firefox, iCal, Adium, Times Reader, Mail), starting a Time Machine Backup, going to a number of different websites, and a few sleep/wake cycles -- we're back to square one with spinning beachball blocks on the order of a minute.
I'm currently trying to isolate the problem, which I suspect may have something to do with Time Machine. Since the recent Snow Leopard performance update was targeted towards performance issues with hard drives, I wonder if that might not still be the issue here.