Phew! I think I finally got rid of everything. *holds breath and crosses fingers* And without calling IT! AdAware would get rid of most stuff, but there were some processes that kept starting over when I would reboot. I manually stopped them and found all of the .exe and .dll files assocaited with them and deleted them. Looking at the modified date really helped because I could see where they all kept re-installing at the same time.
Msconfig does not seem to work on Windows 2000, but through lots of searching and slightly modifying your suggestions, I think I identified all of the nasty culprits. I found some log file in my WINNT/System 32 directory that detailed what was loading at startup and it listed some "unrecognized" dll files that were installed. This is my first time daring to go on the internet since then, and so far, no popups!
Thanks for all of the advice guys, FORT peeps are the greatest.