Open up system preferences and at the bottom, under "Other", see if you have MacFuse installed. I just recently had the same problem of beach balls all the time and finally looked in the Syslog and found megabytes of MacFuse errors. I removed the utility and got my response time back to normal and no more spinning disks.
That being said, MacFuse is a legitimate utility that you might be using. I am not sure why I had it on my system, but so far, nothing has complained that it is missing. Of course, if you take it off and something you need stops working, it is a simple matter to install it again.