Greg Stein (Apache developer and all-around nice guy) made an off-hand comment about open source trademarks in an article(How to Screw Your (Open Source Software) Customers). He was talking about how many users of MySQL have actually using a purchased proprietary licensed copy of the software, and not the open source licensed copy. MySQL's business model uses dual licensing: the GPL, and for the folks whom its strictures are unacceptable, a standard proprietary license. I agree with his point in general: that that's a great way to confuse your customers into thinking that they're using open source software.
I have to disagree with one point he made, which turns on a subtlety of trademark law (but note that I'm not a lawyer; consult one if you would rely on this advice). In my understanding of trademark law, someone may distribute as a part of their software a work whose name is trademarked, and they may say "Contains MySQL(tm)". They may only use the trademark in that manner if they are distributing an exact copy of MySQL. If they combine it with their own code to create a new work, they can't use the trademark that way. They could probably say something like "Derived from MySQL(tm) software".
Trademark law is intended to protect consumers from rip-off copies by giving the trademark holder the right to restrict use of the trademark to their own works. The trademark holder cannot allow the trademark to be used on works whose quality it does not control, e.g. derived works. Hence, the whole brouhaha about the Firefox name and logo not being usable by Debian (which insists on the right to make changes at its whim). Iceweasel is Firefox with Debian's quality control added and Mozilla's removed.
Open source projects that are involved in commerce need to pay attention to trademark issues. If you want to be able to protect the use of your name, you need to make sure that nobody else is allowed to distribute modified versions of your software. You also need to be concerned about the differences in trademark law between countries. In the US, use conveys a trademark. Registration of a trademark you don't use gets you nothing. Nothing. On the other hand, in the EU, use of a name or logo on a product does not grant you trademark rights. Only registration does that.
Complicated? Yes. If you don't care how your project's name is used, then don't worry about it. If you don't care if buggy old versions are distributed under your project's name, then don't worry about it. If you've never made any money off your software (not even a t-shirt sale) and have no plans to, then don't worry about it.