I am so sorry for bothering you people with a lot of questions :'(. This might seem like a very simple question, but I can't find the meaning/use of anywhere. I saw a lot of "Affiliations" sections in a lot of wikis. What are affiliation wikis, and what is their relationship with the other wiki?
It's simply a unofficial cross-promotion thing with wikis with similar subjects. If you have a wiki about a show or franchise, you affiliate with a wiki about another of the creator's shows, or the network's other shows, or shows or franchises aimed at the same audience. Things like that.
It's an opportunity to boost visitor numbers, and at the same time, allow fans to explore new waters.
As you've probably noticed, affiliated wikis are usually listed on the wiki's main page. Some wikis also allow interwiki links between their affiliates in articles to help promote one another. You can be very informal with these links as seen in the interwiki footers (usually network similar shows) or very formal with which the community discusses a nomination and votes on the affiliation. More formal affiliations usually promote the other wiki with a large text logo.