Quoted from Crile1:
I think it more likely represents current market trends and not actual game quality.
I rank this comment #1 on my personal list of Pinside comments on the topic of the Pinside top 100.
Seriously. This is spot on. Game quality is obviously an extremely subjective metric. Every player values things differently, and trends vary over time. The top 100 is purely a popularity contest, which is fine, but should be seen for what it is: a ranking of how much a game is liked relative to other games by a variable community.
On the other hand, it is probably a good indicator of how quickly a given game will sell, and for how much over or under its historical price.