I have some ideas of my own about it, but if anyone knows of an existing
piece of HTML documentation that they found especially usable, I'd find
it useful to study its design.
I do not have any example of "especially usable" design, since I much prefer
the simplest of standard designs. (One page for the table of contents and an
HTML page for each chapter. For chapters with sections, the section names
are given the link-to-location links (<a href="#<location>">). If the
sections get too long, they get separate pages.) Transparent design is best
achieved when the design is really basic. I suspect that looking for an
exceptionally useful design outside of the norm isn't going to turn up
anything.