Perl has neat ways to manage namespaces, so you can avoid singletons, esp for procedural code

If you're going for conditional compilation optimize the code use Devel::CheckOS();
use constant WIN32 => !! Devel::CheckOS::os_is('MicrosoftWindows');

This probably doesn't apply to your codebase, but a common mental block is developing your app in a single file when it naturally lends itself to multiple files

Write/develop/test the code normally in seperate files -- don't complicate development by limited thinking about distribution :)

You can combine it into a single file for distribution later, using fatpack/pp/ http://www.cavapackager.com/ or whatever

PAR/pp can pack your script/modules only without including core modules, but you probably think that's too heavy (requires installing/packing PAR)

fatpack is lighter, and you can fatpack YourApp::Linux/YourApp::Windows, and offer linuxapp.pl/windowsapp.pl downloads

or you can use 'cat' with autosplit/autoload like BrowserUk suggests