I'd be willing to bet it's software for MOST of the issues. I've read a few issues on here like bad drives, memory and stuck pixels that are abviously not common production issues, but something that could happen unfortunately. This could happen with any computer manufacturer you buy from.
I'm currently using a top end last generation iMac 3.06ghz 24in with ATI 4850 card and had a few slowdown problems pop up within the last few weeks after I installed Rosetta. Perhaps my issues aren't common either, but I believe they are related to when I installed Rosetta... since it was flawless before. Rosetta is a software piece that's installed to provide some compatability with much older programs. Best route is to not install it and make sure your using fully Leopard compatable programs moving forward.
My current plan is to live with the random slowdowns until I get my new iMac 27 w/i7 Processor. At that time, I'll format my NEW machine and not include rosetta. Then I'll copy everything over from my old machine. Once that it done, I'll reformat my old iMac Rosetta free and have a few drinks to decide to sell or keep the 24in. I'll probably have a few more drinks because I won't like my decision, so I'll just keep drinking until I realize all is good with the world and I can afford to keep everything I own, since I won't care anymore.
Just my 2 cents!!!