1. Whisper Sun, Silent Moon, by Redsquirrel456
How overlooked is it?: This was posted on Equestria Daily about a month and a half ago, yet the FIMFic page says it still has less than 300 views. For comparison's sake, most stories can get 50-150 views on FIMFic just by existing.
Why it deserves better: This story does an absolutely superb job of creating a wider world in which to exist. There's a fine line between filling one's story with irrelevant, unexplained details and developing an atmosphere of mystery, a sense of knowledge lost to the inexorable passage of time. This story walks that line deftly, and its history feels more alive and engaging to me than any other fanfic I can think of.
Recommendation: The actual story here isn't bad by any stretch either (if it were, it wouldn't be on this list), but I think the biggest draw with this piece is the atmosphere it sets. Any readers who love hinted-at depths in their fiction will probably enjoy this story.
2. Trixies™ , by WaxTomCruise
How overlooked is it?: It was a submission for one of the EqD friend-offs (remember when the fandom was small enough that that could be a thing?), and as far as I know has never been linked to outside of that compilation post.
Why it deserves better: Look, this isn't a great or game-changing story, by any meaningful metric. What it is, however, is a story that makes a stupid (but still pretty amusing, really) joke, then ends before that joke gets stale. Why do so many authors of one-note stories have trouble wrapping up before the comedy turns sour? I don't know, but the least I can do is recognize someone who didn't go in for needless padding. Also, for resisting the urge to tack on some wholly irrelevant aside about how tragic Trixie's backstory is--seriously, why do people write comic short-shorts and then try to squeeze a bunch of angst and drama into them?
Recommendation: Look, if a few hundred words about Trixie playing the role of the Trix bunny sounds funny to you, it probably will be. If not, it probably won't. Personally I thought it was pretty entertaining, and hey: it's like 300 words. If you read it and hate it, at least you didn't waste much time on it.
3. Ties, by Take Flight
How overlooked is it?: This is one that I found a couple months ago while digging through FIMFic's front page. Looks like that was about as much attention as it ever received.
Why it deserves better: To be honest, I just really like the premise. Spike and Prince Blueblood both have their advances rejected by Rarity, and this story shows how each of them deals with that rejection. By keeping the settings as similar as possible, the author hammers home the differences (and similarities) between the two clearly and concisely.
Recommendation: Despite being short and simple, Ties manages to develop both Spike and Blueblood to a surprising degree by playing their reactions side-by-side and letting the reader compare. I'd have no trouble recommending it to the character-study crowd.