Long-shot suggestion: Does dragging the window around the screen immediately cause the beachball to disappear? I had that happen to me once, and I've heard one other report of the same thing here.
if that checks out ok - you know for sure it's not a hardware issue
Actually, you REALLY don't; Apple Hardware Test is always a good first-line thing to try when something is acting very weird, but it's rather notorious for giving a clean bill of health to systems with intermittent problems or certain ones it just doesn't test very thoroughly for.
For example, when doing a drive test it mostly checks the SMART status, but many drives failing with hardware problems will report SMART as just fine. It also doesn't do a really thorough RAM test, and I've had it tell me everything was fine when its
own screen was almost unreadable due to graphics card problems.
As for the OP, do what other people are suggesting. It sounds to me suspiciously like either a hard drive directory problem (which Disk Utility would tell you about, and maybe be able to fix), or bad sectors on the hard drive, which can cause infuriating hangs while the hard drive runs its internal recovery routines.
One thing that might be of interest to check: Assuming here that you don't have an SSD, the next time it beachballs, put your ear on the computer and listen to the hard drive. Is it making no perceptible sound, constant scratching noises, or a rhythmic ticking sound?
The ticking sound indicates a failing drive often--it's the drive repeatedly re-reading the same section of data. The violent scratching sound might be directory problems, Spotlight indexer going nuts, or paging to disk due to insufficient RAM. Dead silence usually means it's hanging in software.
Activity monitor would also show some of the above; if disk access goes to zero during the hangs, it's either bad sectors or pure software; if it goes very high, RAM paging or runaway background processes are more likely.
) then restart and hold down the 'C' key and then run your disk utility repair from there and not from within Mac OSX on normal start-up
