If you have equipped your webcomic with Google Analytics and you host Project Wonderful ads, you have access to two sets of data regarding your site's traffic.
GA gets its clicks via the code that you insert into each page of your site. PW puts its code within the ads you host. Google doesn't count clicks on pages without code, and PW doesn't count clicks on pages without ads.
Many have noticed that PW numbers tend to run a little higher than Google's. Depth of installation would seem to favor Google, since more people put GA code on their inner pages than put ads.
Two possible explanations: many GA users have Google omit them from the count. Google is also said to distinguish and omit spiders and bots. It makes sense that Google would take detection of fake clicks quite seriously, because otherwise their data would be undermined. GA in effect sets a validity floor for PW for free.
Somehow I don't think bots and "ignore users" are enough to explain the difference, and since it's pretty minor anyway, I'll spend my energy on other things. That doesn't mean I wouldn't welcome answers from someone in the know.