Any thoughts on where to look for slow-down nasties?
Er, rather difficult to do sight unseen, there are so many possibilities. If I had the machine in front of me I'd probably find something eventually.
See what the CPU load is and which tasks are using it (nobody would dream of running a PC without Task Manager constantly loaded, would they); see if it's disk bound when it's slow, then see if you're using more virtual than physical memory; if it's disk bound and not thrashing virtual memory then that's going to be more fun to pin down, perfmon might help; see if there's heavy network traffic, or network traffic that you aren't expecting.
(I'm just reacting against the pimply-faced-youth-at-PC-World's advice - for them the answer to everything is "reinstall Windows", because that's all they've been taught how to say. However to reinstall Windows is rarely necessary and quite often won't fix what you wanted fixing anyway.)