Japanese, as I imagine most (if not all) of you are aware, has a pitch accent system, which essentially means that the pitch pattern of a word can be and is often a very important factor in determining its meaning1. As this site grows, I can foresee the number of pitch-accent-related questions increasing, as it is a notoriously difficult concept for many foreigners (especially those coming from non-tonal language -- such as English -- backgrounds).
There are many different methods for showing the pitch accent of a word, from capitalization in romaji (HAshi vs. haSHI) to something which uses some kind of special markup (はし HL vs. はし LH). Of course, the reality of the situation is a little bit more complicated than either of these example systems can really represent without becoming exceedingly unwieldy.
In my speaking and listening classes in Japan, we used one of several formats, two of which are shown in the picture below. The second is one used with several understandings about pitch accent patterns. For example in 標準語: the second mora is always the opposite of the first; and once the pitch accent has dropped in a word, it does not rise again. Please excuse my sloppy handwriting.
How can we best notate pitch accent? Personally, I would prefer some type of markup in Japanese which is easily understood at a glance, but I don't know how possible this is using text.
1 Please see How important is one's pitch when speaking Japanese? for reference.