Last year, I bought a Quad G5 with the stock memory. I did a little research and bought some Geil brand DDR2 memory from Newegg.com. The first 2 gigs worked perfectly first alone, and then with the stock “half gig”. I then ordered another 2 gigs from the same store and I’m sitting pretty with 4.5 GB.
Yes, if there are problems, you should take out the 3rd party memory and do the hardware tests. If the problems persist, and you decide to take the machine to the Apple store, they don’t have to know about the 3rd party memory. If you have done the due diligence and tested without 3rd party memory, I personally think you are in the clear. I’ve not personally heard of a problem where 3rd party memory had damaged a computer. I don’t doubt that it has happened, but I don’t think it is a common problem.