There are so many great regional teams, particularly when you look at their websites.Loving FC Ube Yahhh-man.
There's a team in Hokkaido (the northern island) that has somewhat of a cult following due to its name: Blackpecker Hakodate.
There's also (or used to be, not sure about now) a team whose teamsheet, according to its website, had three players called "Neko-chan" and are cats. Just three to five pictures of their pet cats throughout the senior men's team page.
If I can remember which team it is, I'll look for the page and post a link.