John: I have on my desk a nearly final draft of the Software Freedom Law Center‘s new “Legal Issues Primer for Open Source and Free Software Projects”. The final draft will apparently be made public very shortly, and I think it should answer a lot of your questions. One of the lawyers at the event, in partnership with a major tech publisher, will also be publishing an ‘IP for hackers’-type book in the near future as well.
I will note that the main difference in the particular question you ask (why you can wait to file a patent suit, but not a trademark suit) stems from the different goals of patent and trademark. Trademark’s goal is to be useful to consumers; if a bad trademark is out there, it is believed to harm/confuse all consumers, and must be pursued. Patent’s goal is (primarily) to incentivize inventors, so if inventors want to not pursue violators, that is their call. This is not a complete picture- there are a number of wrinkles on each side- but that is why you get the defaults you do.