Under source control, my scripts are called *.pl. The install procedure moves them into the proper 'bin' directory, removes the '.pl' from their name, adjusts the path to Perl in the #! line, and does "chmod +x". Under Win32, I use pl2bat in place of several of those previous steps.

I never use "script.pl args" nor "perl script args" except for one-offs, because there are times when 'script' gets reimplemented in a different language and I don't want to have to find all the places that use 'script' and change them. For example, I might start with a *.cmd file (same as a *.bat file but I use *.cmd to distinguish them from Perl scripts that have been run through pl2bat) and later add features as part of reimplementing it in Perl.