Computer generally sluggish and apps quick to switch to "(not responding)"

I've had my Mac Pro since last June. I've been becoming steadily unhappy with it. It seems to be running slower and slower and yet I don't think I'm expecting any more from it than before (or even more than I did from my prior Mac, which was a much weaker computer).
The pattern is that I typically have a few programs running and sometimes I'm rendering in the background (i.e. modifying some audio in Audacity). iTunes, Safari and a few other programs will slow down--not a surprise--but way too often nowadays I get the pinwheel and in the Force Quit window these apps will say "(not responding)." After a few minutes, this passes.
I have to stress: I'm not doing anything any differently than I have for years. It just seems that my apps clench up at the drop of a hat. If I'm patient, it passes. But as we all know, to wait 3 or 4 minutes for the pinwheel to disappear is an eternity. (Also, for the money I've spent, it doesn't add up.)
Could I have a virus? Is there one that would give my Mac the computer version of Chronic Fatigue Syndrome? What's the best software to diagnose something like that?
Thanks!

I only suggest this from personal experience. If you have external hard drives connected, dismount and disconnect them. Did this help with the speed? If so, connect your hard drives one at a time and check that they are spinning up as they should. My computer was exhibiting the same symptoms as yours and I determined that the computer was waiting for the hard drive to spin up to speed so it could access it. The power supply for the external hard drive was only producing 9 instead of 12 volts and sometimes the drive would spin up (weakly) right away and sometimes not at all. Replacing the power supply cured the problem.
It is my theory, the hard drive being used for my time machine backups, had to spin up in excess of 10,500 times in 14 months just for time machine. And that doesn't include the times the hard spun up when the computer, for what ever reason, wanted access to it. Although, amazingly, the hard drive can handle all this cycling, I don't think the power supplies were designed for the current loads imposed on them by all this. Somebody suggested deselecting the "put hard drives to sleep when possible" check box in system prefs>energy saver and I found that this further improved the performance as the computer never has to wait for the hard drive to spin up so it can access it.
I hope this helps. If not I don't have any other ideas.
Dave

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