When Gruber mentions that he never uses Markdown outside of his blog, and hinting at the fact that it was not intended for text editors (and other apps), there's one important point I want to make. Yes, Markdown has disadvantages, and a few rough edges for uses as the format for editors et al, but there are two very big advantages and/or sideffects of it's widespread use: (1) it's cleartext and therefore very good as…
Markdown is good enough for most of the documentation that software engineers do (other than diagrams), they already have to know it, and I don't want yet-another-markup-language to be a barrier to capturing and communicating institutional knowledge.
I also tell people that, if you're new to Markdown, even a plain text approximation that doesn't quite format correctly is strongly encouraged, so long as they capture the info somewhere accessible. I'll even offer to cheerfully fix the missing/bad Markdown, so that we have working docs and people can learn the very few parts of Markdown they missed; it's really not much.
(I personally have heavily used many much-much better technical documentation systems, and helped develop a WYSIWYG-ish SGML-based one professionally, but just using Markdown is a no-brainer right now. There are much more important things I want people learning and doing, than N different ways of minimally formatting documentation in N different places.)