With the current news of the Heartbleed bug in OpenSSL security, I was reminded of my old ideas for plot points from back when the Trek producers accepted ideas from fans, though as I recall I didn't really come up with them until after that door was closed.
One was the discovery of a security backdoor in the computer systems of another power. For some reason I associate this with the Klingons, but I'm not sure why. The Federation learning of a Klingon security hole would be a non-story for most of TNG unless you had an NSA-esque Section 31 thing going on. It would make the most sense as a story about the Romulans or Cardassians, and for a modern spin on it with ripped-from-the-headlines effect I could have it as something they knew about and were using against their own people or something.
The trick with any such story is to make computer stuff dramatic, and other than having Picard mulling over what to do with the backdoor there wasn't much drama to it without more work.
The other idea was best set in the Enterprise era and involved a jungle sniper whose beam weapon was tuned to make the beam invisible, and either the planet dampened sensors or the sniper did. The reason it would have been good for Enterprise is that it could've been a Romulan, who naturally would've vaporized himself or been vaporized when capture was imminent.
The thing there is that while a sniper is scary, a sniper who is anywhere in line of sight (or maybe even not, through jungle) and who can vaporize your people is extra-scary. I still like that idea, but it really fits best as a part of the Romulan War.
But, other than being neat hooks, I never really developed the ideas any further. So, author-reading-this, you're welcome. ;-)