Mac Pro CHURNING!

I have a first generation MacPro and it is now a year since I have converted over to mac software now that I have a new mac laptop. Previously I ran bootcamp on the Mac Pro.
In this year I have noticed a relatively loud (for mac) CHURNING sound coming from my MacPro. Oftentimes this is happening when I wake up in the morning. Oftentimes it is almost impossible to get work done due to slowness and pinwheel hangs.
Can anyone recommend some zen and the art of motorcycle maintenance type steps for me to solve this?
Sometime I Cancel Time Machine Backup and it fixes it.
However I also have a Parallels install to access the XP drive in this machine and I notice there is a prlvm that seems to be taking up some CPU.
Now I am using Dropbox to transfer files from the laptop to the desktop and vice versa and I notice this takes up some CPU.
This morning I noticed Carbonite online backup was taking up a lot of CPU.
On top of this I am backing up to secondary external drives using Deja Vu (software is fantastic but tech assistance needs a bit of a jumpstart).
Thanks for any guidance and wisdom.

Hi Grant.
All this is a little tricky here so thanks for the help.
I have Activity Monitor pulled down to Active Processes.
I click on the System Memory pane, yes?
I see % CPU which I think is important (but can't really read intelligently) and I have Real Memory (which I also don't really understand). I also see Threads. Then I see that the User is Root or my Admin name or even _windowserver or _mdnsreponder in one case.
Is there a good way to get it to stop jumping around? Seems like it wants to move the list around a lot
I am not getting the churning after shutdown but
Kernel Task is using 306.6 MB which I guess is totally inconsequential, it has 70 threads and CPU is 1.5% (my top listing at the moment). Obviously not a problem as it is quiet as can be but if I can get a handle on some of those perhaps I can tackle it better next time?
Can I ask you how I know if I have had a page out?
Also, at one point someone asked me to open something a little like Activity Manager to see if there were a lot of errors generated. Do you know if this was a history record of some kind or what this utility may have been?
Thanks a ton.

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I'm in the video industry, so I share your concerns.
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