Trademarks are actually still useful for open-source software, since they ensure that a malicious or incompetent party can't ruin the name of your software by shipping a modification that does bad things.

Jason Rohrer ran into this very issue when other developers made their own client for his game, using a variation on the game's name. They didn't respond to him asking that they don't use the name, and eventually he was convinced that trademarking the name is the right tool to project it. The original game client is still open-source (and maybe the server too, dunno).