While the advice above on refactoring is certainly excellent, and probably the best in the long run, you may also consider using an infrustructure like Apache's mod_perl. Sometimes, the porting of a system to mod_perl can be faster than refactoring all those modules.

It also might be the right thing to do. The fact that most modules need to be loaded most of the time might not be a sign of bad design, and moving to a persistant architecture could well be the best, as well as possibly (depending on how much the current system relies on having a clean slate between runs) the simplest, solution.