The Github API rate limiting made it impossible to keep up with the user/repository growth so I stopped in March 2012. Only users that were public at the date of the crawl, and are part of the largest connected component of the network will be shown.
I am the designer of Ekisto. Questions and feedback are welcome :)
Random suggestion: mapping a user metric such as dominant programming language to inform the building style. So maybe shell code would be more oldschool (Chinese/Japanese/Korean style wooden pagoda type look), perl would be hacky (like lashings of bamboo), enterprisey languages would be shiny skyscraper windows, and obscure stuff would be mud brick or straw bale or something!
The spatial proximity domain seems a little wasted with this mapping .. perhaps it could be improved by using direct links informed by real clones/contributions.
I hope Github gives you a data feed!
You are spot on that Github has very rich relationships of collaboration and sharing that are not all expressed by the data I chose. I wrote a longer post about my goals and motivation with Ekisto that addresses that concern: http://processq.tumblr.com/post/69098066993/ekisto-design
I also write about future work which will improve the current version. I think some tagging functionality either precomputed or user-contributed will help a lot of newcomers understand the map better. Stackoverflow veterans immediately recognize the clusters and the avatars.