Trademarks are an important part of commercialising or sustaining an open source project. A TradeMark is the "brand" created by your project.
Choosing a Trademark
The more descriptive the trademark is, the less valuable the trademark. Think of the strong brands in the IT and open source sector today. For example, Google, Apache, Firefox, Yahoo! - they are all strong trademarks but they do not describe the company, goods or services they are applied to (true people "google" the Internet, but try looking Google up in a dictionary).
Look around using all the tools at your disposal for similar or competitive software projects. Ensure that your proposed trademark is not confusingly similar to a name used for that similar software. If you have any doubts ask for legal advice. As with all legal issues, it is better to err on the side of caution; don't pick a trademark that looks or sounds confusingly similar to an existing trademark for software.
Claim your mark
Don't be secretive about your trademark. It should be promoted as the way, we mean the one and only way to identify your software. Put a "TM" by it in its first use within any document.
Register your mark with the appropriate registries.
If anyone complains that your mark infringes on their mark do not respond to the claim. Seek advice immediately.
If you feel someone else is infringing your mark do not contact them. Seek advice immediately.