I suggest staying away from the "Username::*" naming convention. If you decide later you like it well enough to publish it on CPAN then you'll have to rename it.

Version control systems are useful, and definitely a good idea even on solo projects (I'm a fan of RCS these days, largely because I live inside of emacs... checking something into RCS is just 3 keystrokes: "C-x v v"), but I'm at a loss as to how version control would make it easier to find a module.

I think the original poster really needs better ways of searching his disk... I keep meaning to play with swish-e, myself, but in the meantime I fall back on find/greps of various sorts.

Of course, a better organizational strategy wouldn't hurt, but there really isn't any one right way of doing these things...