Just finished "Predetermined Coincidences" by Dewey001 and wanted to extoll it's virtues. Combines action and a good storyline with familiar elements from a couple of Trek flicks. Great mission deserving of Spotlight status. Make it so!
For the moment, I cannot post my favorite 5 as I only have a ONE favorite SERIES! The series is call ST: Odyssey by dariuskoronikov. This series starts with the trilogy: The Olympus Trilogy and lasts the span of 40 episodes total (including the three of the trilogy itself). This series actually gave me the final inspiration to write my own series (which is still in the works right now), and I have had communications with dariuskoronikov, who has given me his permission to use his series' characters in my own series (with a few provisoes, of course). I will let you know what the status of the series is when I am super-close to publishing the first episode (which may be a while)!
"Relics" by Kirkfat, for good use of the interaction between religion and Trek-level science, good use of map-altering triggers (which ought to be a given, seeing as it comes from the guy who wrote most of the tutorials on them), inadvertent* lesbian flirting between my captain and an NPC (which just made me laugh), and brilliant use of lampshade hanging. I liked it so much I wrote a page for it on TV Tropes.
"One Too Many" by XR-377, for hilarious parody of many a Foundry and Star Trek Online standby and another inadvertent lesbian (accounted for in a dialog option this time!).
"In the Shadow of MIDAS, Part 1" by thegreendragoon1. Good call back to late Voyager, good dialog writing and map design, and bonus points for prompt and gracious response to me pointing out a plot hole.
The "Dark Alliance" series by skydawnknight, particularly "Dark Alliance 2: Black Spiral". The allusions to a noodle incident involving my PC and Saria were very intriguing, and the various side interactions in the Aurora lounge were hilarious. Also, good use of reskinned mobs throughout and good dialog.
* "Inadvertent" due to the Foundry lacking gender-operated dialog tags.