I'm fairly sure that list is populated by the highest rating scores, and the amount of votes a show receives is totally irrelevant. Shows that are popular also have a lot of trolls, who give the show a zero rating, and artificially lower the score, while fanboys give it a 10 and artificially raise the score.
Relatively few people have seen shows like Mushishi and Nodame Cantabile, and they don't have a lot of acclaim, so the people who enjoyed them, which make up the majority of the fanbase, rate them highly, and the trolls largely aren't an issue.
Basically their ranking system is flawed and stupid, and that list is meaningless. Even if their ranking system wasn't flawed and stupid, the list would still be meaningless as a measure of quality, and would only be a measure of general opinion.