I have been experiencing the same issue on a 2011 imac running 10.6.8,
Model Name: iMac
Model Identifier: iMac11,3
Processor Name: Intel Core i3
Processor Speed: 3.2 GHz
Number Of Processors: 1
Total Number Of Cores: 2
L2 Cache (per core): 256 KB
L3 Cache: 4 MB
Memory: 12 GB
Processor Interconnect Speed: 5.86 GT/s
Boot ROM Version: IM112.0057.B00
SMC Version (system): 1.59f2
where the cursor turns into a spinning beach ball, and safari freezes and mouse clicks are ignored until the cursor is clicked outside its window (on the desktop) and having gone through the whole system (applications etc) looking for a solution I have found that the problem really only occurs when a legacy Power PC program was run and can now recall Rosetta firing up when it was installed and run for the first time.
When the cursor problem is apparent the application, an older accounting program run by another user is usually open, closing this and restarting the iMac resolves the problem and everything works OK, no stalled Safari or cursor problems experienced, restart the accounting program and eventually the cursor and Safari problems return.
I'll leave the group to ponder if they have any legacy applications that invoke the use of Rosetta in the background and create a similar situation.
A Mac Pro I use running all CS5 Suite etc, has no such problem with Safari etc, but that is free of any old legacy applications that require Rosetta.
Its all a bit of a mystery, but clearly is very prevalent if you study all the results of a search for cursor problems on Mac OSX. Perhaps one day someone will offer a definitive answer and solution, won't be holding my breath though...... ;-(