Just came across a new version of Prime95 v25.1 http://www.mersenneforum.org/showthread.php?t=6572 which seems to be multi threaded! It even recognises my Core 2 Quad Q6600 Kentsfield's 4 cpus.
For stressing cpu, you can run 4 threads for each of 4 cpu cores i.e. Small FFTs. Only limitation i find is if you want to use custom blend to test >2GB of memory, i.e. 4GB ram you need to run 2 instances of Prime95 v25.1 with 1350-1399MB assigned to each instance of Prime95 v25.1 as it has same limitations of 1.5GB per process even with /3GB boot.in switch enabled on WinXP Pro SP2 32bit.
2x Prime95 v25.1 instance with 2 threads per instance
Assigning 2 threads per instance and then setting each of the 2 threads to each of the 4 cpu cores
Did the above for 2 processes to confirm whether or not assigning affinity in Prime95 v25.1 works and it does
1x Prime95 v25.1 instance with 4 threads
One instance with 4 threads tested. The settings:
Running small ffts
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