If you design your application right, it shouldn't matter which you choose.
A big point might be the versions of various modules that each can provide, or not provide. PPM packages can lag behind CPAN releases, but if you aren't careful, bleeding-edge CPAN releases can break backwards compatibility. Furthermore, sometimes there will be PPM packages for things that just won't build properly under Strawberry Perl (though this implies that the module is poorly designed more often than not).
Just be aware of the versions of any modules you use, and you should be fine, regardless of which you choose.
