By dint of poking around in Daypop's citations I ran across Nicholas Jon's blogosphere.us. On the surface, blogosphere.us looks to be similar to Blogdex and Daypop, but as is usual, its techniques aren't documented.
Update: found a bit more info in another somewhat incestuous article, and its more detailed version.
Careful readers will note the implication that Daypop uses sites that index citations as part of its citation count (apparently). Whether this is a good idea or not is left as an exercise to the reader.