I have recently been experiencing what I thought to be freezes. However I noticed that programs continued to function normally and discovered that unplugging the keyboard and plugging it back in fixes the problem. This fix only works temporarily and the problem occurs again after some time.
Problem occurs in various programs and in Finder.
I recently went through disc first aid and repaired permissions although I'm not too sure if this is relevant.

I've seen a similar thing on a MAcOS 9.2 machine - thought the issue was withthe mouse, it was otherwise the same. Replacing the mouse and keyboard did not help, unfortunately. I was very reluctant to erase and rebuild the machine (the next step after everything else I'd tried, ie PRAM zap, prefs nuking, etc), as it would take me quite some time - think Quark, Photoshop, etc etc on a DTP workstation. I eventually swapped the hard drive into another machine to see if it was a hardware fault.

The result was indeterminate - the problem never resurfaced on the original hardware _or_ the replacement with the original hard drive. I'd love to know what caused it, but at least it's gone away.

I'm not sure this is really useful to you, but I thought I'd let you know that I, too, have seen intermittent USB problems with basic devices on Apple hardware. Perhaps you might want to drop in a PCI USB card to see if that helps (assuming Macs support them properly - anybody know?).

Craig Ringer