goodness, i really have to stop procrastinating and get out of the house. but anyway, i am assuming you are using leopard. the culprit is not just appfresh, if you browse around the apple support forums and others, you'll notice that many sparkle applications cause this issue. on leopard there was a change to how the launchservices database works, along with being moved to a different location, it apparently does not update/refresh too often, so when one moves an older version of an application to the trash and places a new version in the original location, launchservices will store the newer version's information in its database atop of the old version, causing the "open with" menu to become cluttered with duplicates of the offending applications. the fix is simple;
launch terminal, paste the following text into it and hit enter;
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain userthen log out and log back in, now the issue should be resolved.