I haven't paid for advertising over at Top Web Comics yet, but I plan to eventually. I get a fair amount of traffic from them just by having my comic listed! So yeah, that's probably worth it.
Project Wonderful is okay...but again I've only really had experience with free advertising there so far. It would probably be less cost-effective than TWC.
Best Webcomics also has advertising slots, but again I think TWC would be the most cost effective.