I use Markdown; not necessarily because it's the best, but because that's the closest thing to "standard" there is today. Stack Overflow, GitHub, BitBucket, and reddit use it.
I find that switching markup languages is annoying as half the time you're typing in the wrong language. It's mostly intuitive, but there are some annoyances (like different behaviours across implementations).
I used txt2tags for a while (many of my posts in "Guides" are written by it), but switched to markdown as I didn't want to change between three markup languages (Markdown, txt2tags, Wiki). It hasn't received updates since 2010, so it seems rather dead. The chief advantage of markdown is increased flexibility, although depending on which markdown converted you use, this can also be achieved with Markdown.
reStructuredText and Textile are two other alternatives. I never used either.
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UNIX was not designed to stop you from doing stupid things, because that would also stop you from doing clever things.
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