The list updates net gains in active installs, so it's a trend measurement, versus total active installs or downloads. That's what accounts for some of the large variations between weeks. From the announcement, their justification for the list:
As committed members of the WordPress community, we thought it would be helpful for everyone to see what customers are really using from the world’s biggest WordPress hosting provider to help everyone recognize the trends in the market. There is a transparency in open source projects (especially in WordPress) that we think is really healthy, and we hope this is useful for small businesses, web developers and the WordPress plugin and theme community at large.
Most of the results are still pretty big plugins and themes, but not all. Also, the lists also include commercial products, so you can see products like Gravity Forms and Genesis side by side with free ones, which is super interesting.
Props to GoDaddy for putting this together. I love seeing it. However, it makes me hungry for total active install counts. 🙂