I've recently had to read several thousands of lines of C++.

Doxygen and cscope made me very very very happy. It beat paper even on screen because I can read the code in the doxygen format, view weird hierarchies (class, file, function calls), and when I think I know where I'm going to investigate vim with cscope is an easy way to help your brain emulate a callstack.

I haven't ever needed to go through this process at such a scale with Perl code, but i will be searching for such capabilities when I do.