Generally speaking (for the pendants), the current way we identify files on desktop OSs is filename extensions. It didn't used to be this way Smithers, many OSs including Mac OS and *nix could identify files without them. Another unfortunate legacy of having to support Windows.
This morning our time, John Gruber elaborated on the lack of an official Markdown filename extension. He endorses ".markdown", agreeing with Hilton Lipschitz that "we should be using the most descriptive file extensions".
I can empathise, but I employ ".md" precisely because it's succinct. NetsecReport.md is more useful to me than Netsec…ort.markdown as viewed in the Finder's column view, or TextMate's file browser.
This does create a little more work for us developing software, but I see this flexibility as a strength of this plain text format, rather than a weakness.