caveat: not necessarily a direct answer

If you're not already using it, CVS may be of some benefit in organizing your code, with The CVS (free online) Book being a good tutorial.   A Monastery search on 'cvs' also turns up a passel o'hits, hopefully some being relevant.
    cheers,
    Don
    striving toward Perl Adept
    (it's pronounced "why-bick")

Update A: to more directly answer your question, I keep current executable versions of my own scripts/programs in a structure pretty much like what you expressed dissatisfaction with, and experience some of those same concerns.

~/bin/bash/
     /java/
     /perl/
[download]

Fwiw, I try to give my scripts/programs descriptive names, to make it easier on my feeble recall.   Although this often runs counter to the principle of short-names-for-oft-used-tools.   *shrug*   In addition, I try to use one-liners when possible, rather than writing piles of throw-away snippets.   Seems to help a bit in avoiding clutter in ~/bin/perl/ directory.

Update II: For what little programming I do on Win32, I've yet to need anything more complex than this:
c:\perl   Perl install of course
c:\perls   for my scripts/programs

Like you, hoping to hear how other other monks do it...

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