The size of your codebase is definitely not the issue here. We have ~38000 lines of code spread across ~150 modules that load up under mod_perl. We maintain database connections to Postgres, MySQL, and Oracle and use each extensively. Our code executes very quickly and we have excellent site performance. However, because we are running under mod_perl, we are not going through the overhead of compiling the code with each request.

You did not specify that this was CGI, so I'm going to assume that you are talking about command-line type scripts. You are loosing time with compiling the code every time you execute it. You could take the approach of breaking you libraries into smaller libraries that are grouped in some way that works well for your needs. You could then just require the needed libraries when the need arises.