I've noticed quite a few Mac and iOS apps using Markdown lately. If anything it seems to be gaining adoption. Of course this isn't based on any actual data just my own observations. Perhaps a Windows user can chime in and comment about it's growth from their perspective.

I'd love to see it being used in more blog commenting systems.

Perhaps not a lot, but certainly a few heavily-used apps and sites use something resembling Markdown. Namely, Github, HN, and reddit.

The original Perl script gets very little use, but the formatting conventions established by Markdown have become enormously popular the past few years, displacing older conventions like BBCode.

Some implementations (like the one here on HN) support only a couple of features. It's more of an archetype than a proper standard.