Markdown syntax is used for comments, analyses, About Me's, and forum signatures. See here for how Markdown generally works.
Some parts of Markdown are not used on Sedecology. Embedding images is disabled, and you can't use HTML tags. Headers are limited in length to avoid abuse of the large text.
Replies and mentions
Highlighting syntax (==text== with two equal signs on both sides) is repurposed for replying to comments and analyses. The first number that occurs inside will be interpreted as a comment id, unless it is preceded by A or A# in which case it will refer to a typing that has an analysis attached. The output will show the person you're replying to and everything other than the number will be ignored.
Currently notifications are sent for mentions and replies but only inside comments, not analyses or About Me's. For this reason, when you quote something the reply links will be escaped like ==/text== and the mentions will be escaped like @/user -- the links will still work but the slash will deactivate the notification. You can add a slash yourself too, if you don't want to bug people. Only a limited number of notifications will be sent per comment. Editing a comment updates the forward links but will not send new notifications.
Cross-thread replies are also fully supported.
Spoilers
Spoiler syntax is like ~~this~~ (which is normally the syntax for strikethrough), it is toggleable and will also be hidden with [spoiler] in the event feed which does not normally render markdown. Spoilers can go across lines in the markdown but cannot include an empty line (which separates paragraphs).
Other
Basic features like bold, italics, quotes, and links will probably stay the same, but other syntax may be repurposed or disabled in the future, such as indented code blocks and backticks.