A key issue for handling of bopomofo (zhùyīn fúhào) is the placement of tone marks. When bopomofo text runs vertically (either on its own, or as a phonetic annotation), some smarts are needed to display tone marks in the right place. This may also be required (though with different rules) for bopomofo when used horizontally for phonetic annotations (ie. above a base character), but not in all such cases. However, when bopomofo is written horizontally in any other situation (ie. when not written above a base character), the tone mark typically follows the last bopomofo letter in the syllable, with no special handling.
From time to time questions are raised on W3C mailing lists about how to implement phonetic annotations in bopomofo. Participants in these discussions need a good understanding of the various complexities of bopomofo rendering.
To help with that, I just uploaded a new Web page Bopomofo on the Web. The aim is to provide background information, and carry useful ideas from one discussion to the next. I also add some personal thoughts on implementation alternatives, given current data.
I intend to update the page from time to time, as new information becomes available.