I think of Freshmeat as a site for *nix (mostly Linux) related apps. Freshmeat's name doesn't exactly say what the site is for, just like slashdot doesn't... Both are in danger of changing loyalties at any moment. This could be a good thing if you think "business"-wise. For instance, this could mean that the owner(s) of Freshmeat could turn it into an online shopping mall and ditch open source and make big money, which would be positive for them.
It could also turn into a BeOS-only or Win32-only site, or whatever. Sure, everyone says we should allow any OS to be fair... but, as someone pointed out Freshmeat allows proprietary licenses to show up. Freshmeat has been very Linux biased which is why you see so many GPL'd apps (with a few commercial and non-OSS software showing up), take that away and you'll find a lot more proprietary applications getting registered.
Here's my solution. If you want to include other OS's and be fair, then stop allowing proprietary applications. (Also, set up different sections for different OSs, and possibly "multiplatform" sections, a lot of Linux apps are multiplatform already, says something doesn't it?) If you want to allow proprietary applications, then align with Linux-only or be prepared to turn into a non-OSS site.