The best replacement for markdown is textile.

The best alternatives to markdown are rated as following:
★★★★★  textile
★★★  markup
★★★  restructuredtext
★★★  asciidoc
★★★  latex
★★★  discount
★★  wysiwyg
★★  bbcode
★★  rst
★  org mode
★  wiki markup
★  mediawiki
★  multimarkdown
★  creole
  rdoc
  haml

Your alternative for markdown is not listed? Suggest!
Speaking about markdown, one probably shouldn't forget about evernote.

Other search terms related to markdown and their ratings are:
★★★★★ evernote
★★ footnotes
★ mathjax
You have in mind a companion for markdown and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of markdown in all years. Click on graph for more.
markdown
textile
markup