I like to keep each project in it's own directory. I have a big directory called ~/apps/dev/ with a bunch of project directories. I have a directory in there called scripts/ for my often used mess of perl and shell scripts. I also have an oldscripts/ directory which contains stuff from scripts/ I don't use any more.

The tree looks something like so:

~/apps/dev/
           oldscripts/
           project1/
           project2/
           scripts/

Hope this helps. :)

PS: as ybiC mentioned, version control is always quite helpful. I have used CVS to manage my perl scripts for years, and it works quite well. Lately I've also been playing with Subversion, and it seems to work quite nicely too. One really nice thing about Subversion is versioned renames, which allows me to move my stuff from scripts/ into oldscripts/ easily.

Update: another small point I forgot to mention is I don't execute scripts directly out of ~/apps/dev/scripts/. I make symlinks into ~/scripts/ (which is in my path). This way I can be a bit more picky, and only link to the scripts I actually use (this code tree is shared across multiple machines). This also helps me decide what to move into oldscripts/... if something isn't symlinked anywhere, it goes byebye. :)