Popups are very difficult to eliminate entirely since 1) they're usually brought up by JavaScript on a web page and so not amenable to easy blocking - the built-in popup blocker in browsers usually won't stop these - without turning off JS and 2) the sites often move around and so are difficult to get a good pattern on for creating a block script in GlimmerBlocker. You can try to create a filter yourself, and GlimmerBlocker has some additional filters here that might help:
http://glimmerblocker.org/wiki/Filters
but often they'll block content you want, so as Allan said it may not be worth the effort unless you're just being plagued with popups in the sites you visit (I might mention that I've never come across a MacKeeper popup myself, so either GlimmerBlocker is doing a better job for me or we just travel in very different web circles).
Regards.