I'm no neatnik, But I can relate to WANTING to be more organized.
Its a good question as it can be a serious difficulty.
My efforts at this are ever evolving, but the first thing for me is as you say- naming everything with a purpose.
My current system is a naming convention that begins with a description I can decipher, say "Ac Guit" "Ld Guit" "3rd Kazoo" etc. You get the idea.
Next its a letter designation if there are multiple parts or sections for that instrument.
Lastly
if there are multiple takes I use a number to keep track.
So I end up with something like "Ac Guit A3" or similar.
Next, (and many will object to this)..... I tend more and more to NOT save so much stuff. I pick a take or version and commit to it, and generally purge the unused. Yep.
And I am not big on recording take after take. If a few wont capture a usable recording, somebody (often me) needs to go work on the part and try again later. Maybe that's just me.
But I have found if I save all my takes and every little effort I end up with a bunch of extra stuff I will never sort through again. So once I have chosen parts, edited and gotten to the stage of rough mix, the extra stuff gets purged. The only exception is if its a particularly "special" project, then I might create a backup folder with everything I wish to archive, and duplicate just what I need to a "working folder"
I also admit that most of my projects are just not that large track count and file wise as to become as big a problem as say Chibear's orchestrations. A typical project for me might be for example in the 20 tracks range, and given that, the above naming and purging usually creates a manageable folder.