As far as english-speaking site go, people see geocities, tripod, anglefire, homestead used to be one, ect. sites as lower quality because they have a reputation for having simple fan sites, or just sites made by inexperienced people in general. Not only because they're free, but because they have those "easy page maker" things, which generally don't make pages look professional unless you work pretty hard on it. Also, the pop up ads, and corner geocities ads are looked down upon in general, the closest to those that are acceptable on big sites are the ads put there by the owners to make money.
So, in the end it just all comes down to the free hosts having a big history of running a bunch of kids' Yu-Gi-Oh sites when they were 10 years old, and just seeing geocities as the host of the page knocks down it's credibility to some people, almost no serious large site would ever affiliate with a link from geocities, but that might be because people don't start sites that they expect to be respected by others on geocities to begin with.