I recently applied for registration of the Finnix trademark with the USPTO. Registration is a long process, and should be completed in 13 to 18 months. Of course this doesn't mean that I am not allowed to use the name "Finnix" yet; rather, trademark registration is designed to give you more power in asserting ownership of a mark for specific purposes (in this case, use of the name "Finnix" relating to "computer software", dating back to 1999).
If you have an even moderately popular open source project, I would strongly suggest looking into trademark registration. Registration is $275, but worth it, especially considering recent headlines. You can hire a lawyer to do the work for you, but the USPTO does have a relatively simple "self-service" application for registrations. I used their online tools for searching for existing trademarks (nothing comes even close to the name "Finnix"), and spent about an hour filling out paperwork.