I have the refurb 1.6GHz, 80GB and have not noticed any stuttering or heat problems. It was totally worth the $999, but for me it's nothing more than a portable machine, not my main computer. If I'm doing something terribly intensive, I'm probably doing it on my iMac (home) or Mac Pro (work).
I'm wondering if Apple actually did to something to the refurbed Rev A models, because I don't have any major problems with overheating either. I do use coolbook though, but hulu never stutters and although the back/bottom does get pretty warm, it hasn't shut down a core yet. I've put it through its paces and I am reasonably happy so far.