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Yes, it will test whatever memory you have. My PowerBook was freezing all of the time so I ran my Hardware Test CD and it found my new memory to be bad. I replaced it (under warranty) and I've never had a problem since.
 
It would be rather silly for the Apple Hardware Test not to verify third party memory, considering that Apple doesn't manufacture memory at all. All memory used in Macs is manufactured by some third party.
 
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