Okay, so it's not really software-centric, but man, do I feel like a dope.
I have spent about 12 hours over the last three days trying to rid myself of what I thought was spyware being constantly invoked by a trojan. I even deleted and reinstalled Firefox because it spawned windows that Explorer did not, even when i followed the same paths.
I kept getting a window that said, "Zedo blah blah." Turns out boston.com has this embedded in some of their pages and Firefox doesn't kill the popup.
This seems to be a fairly common problem. I am currently downloading Firefox's adblaster plugin to take care of these windows.
Always the most obvious solution, huh?