We've somewhat adopted markdown syntax to our purposes
Quoting
We tend to use two different mechanisms for 'quoting' bits of Japanese in the middle of english text. The first is the backtick format for inline japanese. Note that the furigana inserter does work with this syntax, since it implemented as a client-side javascript formatter.
For larger sections of example text, we prefer to use the block-quote syntax over the pre-formatted text. One reason for this is that text, unlike code, usually can line-wrap freely, and the formatting is not nearly as important as the content. It's also somewhat easier to work with. This entire section was block quoted by using a single '>'.
Linking to Japanese URLs
If you insert URLs directly into markdown, you may run into issues with the japanese characters being ignored by the auto-URL parser.
The easiest solution is to use the link button on the edit screen, as that will convert the URL to a properly encoded form.
Discussion
Bold Text Embedded in Japanese Text
It can be convenient to bold certain parts of a sentence for focus. Unfortunately there is a markdown bug that can sometimes cause words not to be properly bolded unless they are surrounded by spaces. Since the Japanese language does not generally use spaces, this hits us harder than most sites. This bug has been particularly nasty in the past, as it has not shown up in the preview pane, but does show up in the final text.
A workaround is to use the "some<b>text</b>here" syntax which will produce -> "sometexthere"
Note that if you are trying to bold text using the furigana system, you currently must bold the ENTIRE block with syntax like this: <b>[漢字]{かんじ}</b> in order to get [漢字]{かんじ}. Attempting to bold only part of the text in the furigana 'unit' will not work.