Trademarks, unless abused, are intended to protect consumers' interests—are they getting the brand that they think they're getting? If you download Firefox, are you getting Firefox, or a derivative?
Firefox is precicely one of those things that has brought this issue to light for me personally: the name is trademarked and derivatives must use their own names, leading to IceCat, IceWeasel, Abrowser, etc. Even though FF is free software, the trademark imposes additional restrictions that seem contrary to the free software philosophy. As such, it was my opinion that trademarks should be avoided or, if they exist, should not be exercised. (GNU, for example, is trademarked, but the FSF certainly does not exercise it; consider GNUplot, a highly popular graphing program, which is not even part of the GNU project.)
I recommend that trademarks not be used for free software projects, though I am not necessarily opposed to registering a trademark "just in case" (for example, to prevent others from maliciously attempting to register a trademark for your project).
 uspto.gov; serial number 85380218; reg. number 4125065*
* From what I could find from the USPTO website, it was submitted by Aaron Williamson of the SFLC (http://www.softwarefreedom.org/about/team/)