Help! Stutter problems with 10.6.8 MacPro early 2008

I'm running 10.6.8 on an early 2008 Mac Pro.

My problem is that recently everything has gone "stuttery" 😕 :

• Running a video through Youtube gives a 0.5sec video freeze every 30sec,

• Opening up MacRumors webpages displays the first half of a forum page, then it hangs for 1-2 sec before displaying the rest.

• Scrolling through Finder windows isn't smooth

• Using time machine takes longer than 1 hour to perform even small hourly backups so is in constant use (problem exists even with TM turned off)

* Checking Activity monitor I don't have any rogue processes running.

• Bootdisk still has 275Gb free.

* Logging in to the computer as a new account doesn't give these problems so I'm ruling out a graphics card/hardware/HDD problem.

When I got this computer, new, 4 years ago I used migration assistant to grab the contents off my previous Mac. As a result I have shed loads of stuff on here but the problem only started in the last month. I haven't installed anything I can think of in that time. Due to the above criteria I'm convinced it's something running in the background that's corrupt (Java?) rather than a hardware issue, but with so many files on my system I don't know where to start (and I don't want to erase stuff randomly until it stops!)

Can anyone suggest a diagnostic procedure/app to help track down what's causing this really irritating stutter on my Mac?

Thanks