Anyway, below the break are links to the stories, brief descriptions of what's so good about them, and a recommendation. Enjoy, and I hope you find something here you haven't seen before.
1. Duke Lionheart, by JimDimitri
How overlooked is it?: Well, I first saw it when a link got posted on /co/. The ff.net page where it's located has all of...wait for it...2 reviews.
Why it deserves better: Writing something bad is easy. Writing something so bad it's funny is hard. Although I know many people "enjoyed" it, I found Spiderses to be completely unbearable, and have not been impressed by other attempts at so-bad-it's-good fanfics.
Duke Lionheart is an absurd and nonsensical tale filled with bad writing and worse dialogue, and I loved every word of it. Part of its success is in its brevity: at only a few hundred words, this story doesn't stick around long enough for its shtick to become repetitive and grating. The other thing that draws me to it is the compactness of its humor. Every line is funny, the story lacking any sort of plodding filler (I just went back and double checked; every single sentence is funny. Scout's honor). Reading this story is eighty seconds of gut-busting mirth--a worthy experience in my book.
Recommendation: If you like goofy, illogical humor, coupled with the most ridiculous "world building" ever to grace a computer screen, give this a look. Hey, it's like half a page long--if you don't like it, at least you won't have wasted much time on it, right?
2. The Liar, by Chopper's Top Hat
How overlooked is it?: It was put up on Equestria Daily...where it received 11 star ratings and five comments, one of which was a reply by the author.Why it deserves better: In this fic, the chronology of paragraphs is reversed. That is to say, the first paragraph is the most recent, and the last paragraph of the story is the "beginning." If that sounds confusing as hell, it is. But it's also a highly satisfying puzzle of a tale.
After I read this story, the first thing I did was go back and read it again. Not because I was confused (though there were things I only caught the second time through), but because I wanted to take part in that puzzle again. Now that I knew the destination, I wanted to see how it was put together; to test its springs, so to speak. I think re-reading a story is one of the highest complements you can pay an author, and this is a story that positively demands that the reader come again.
And even without the gimmick (skillfully done though it was), the story stands on its own. Trixie's backstory is well-conceived, making her almost pitiable without absolving her of any responsibility for her actions, nor taking her out of character for the sake of making her "relatable."
Recommendation: This is not a fic you can skim through and expect to get anything out of it. But if you're willing to make the effort to follow this story, it will reward you with a sad and chilling tale that unashamedly requires (and repays) careful reading.
3. Pony Magic, by CttCJim
How overlooked is it?: Well, the Deviantart page where it's posted has ZERO replies. Honestly, I don't even remember how or where I found it, but I like it enough to save the link.
Why it deserves better: There have been several authors in this fandom who have written stories which take the form of scientific papers. I know that some folks find these to collectively be too dry and "science-y" to enjoy, but I've always had a soft spot for them. For my money, the best to date is "On the Nature of Anomalous Magic Levels Surrounding the Everfree Forest," but this one has a lot to recommend it as well.
Although it's not as humorous as many attempts at faux-research papers, Pony Magic takes on questions about how magic functions in Equestria, as well as side issues like what happened to Twilight the day she hatched Spike, and spins them into a very readable collection of notes. The style isn't as rigid as some, but this fits its backstory as a set of notes collected by the Princess herself, rather than a published piece of work.
Recommendation: If you don't like "scientific papers" as a genera, then obviously this story isn't for you. If you're like me, however, you'll find the explanations of Equestrian biology and sociology contained herein to be a fascinating read.