I am feeling a bit crazy after reading this thread.

I re-installed the system but still have the same issue. I found that spinning balls always appear only during the start of applications, especially heavy applications like Open Office, but never in the middle. More specifically, they always appear during the cold start, after re-booting of MBP, but I do not remember if I see them on second and following runs of the same application. Today, I saw beach balls during the start of Photo Booth, Automator, Fink Commander, Portal. How often do you notice this behavior on your system? Should I bring my MBP to the Apple store?
Recently, I compiled few applications in Fink and watched movies. Several times without any problems, no freezes, no beach balls in the middle. Temp. was around 65 - 75 C. My old HP runs at 90 - 95 during compilations and without movies.