I used to play an MMO called City of Heroes/Villians, and I would always hang out in a place called Atlas Park, so I named my town after that, my town flag is also based on the games logo. The game has sadly been shut down.
Snowvile. Meant to be snowville. I came up with it super quickly when I started city folk because I just wanted to play and figured I'd reuse it in new leaf.
I have 3 towns. Primrose, Yukino and Highland. I did have a 4th but I gave the cartridge to my daughters friend in trade for her town lol. I loved her map.
Skullbay. I decided long before the western release of the game that I would make my mayor a pirate, so i thought that Skullbay would be a fitting name for my town.
Fortree, named after the city in Pokemon Ruby and Sapphire. I thought about a few other pokemon related names and I wasn't so sure about this but now I really like it.