Someone asked me if I could name one story I love, but which does not get enough attention.

I can't, for two reasons:

A: I don't have that good of a grasp on what is popular, exept from some very well known tales and the feature box.

B: THERE ARE JUST SO MANY!

So here is most of them, with a short description.

No particular order, categorized by what I believe to be the most noticeable tag.

Romance:

Near Death Experience by Hadles

Quite an interesting romance: A pony falls in love with the grim reaper. He, however, has no idea what ponies... well, DO. Except die.

It has a dark tag, which is appropriate: ponies do die in this, and there is some gore. not too much though, and rarely permanently.

Learning ABCs - Adorable, Bothersome, Chaotic by Klabautermann

Twilight x Discord. Humorous, cute and of course, slightly chaotic. Discord has to move in with twilight to learn about friendship. stuff ensues.

Sketchy Salad Symphony by Sketchy Sounds

I really, really love this one. Laid back atmosphere, great characters, beautifully written. Especially the banter.

This is just as much a slice of life as it is a romance. No mane 6 at all, which is refreshing.

Shipping and Handling by Pegasus Rescue Brigade

Ditzy/derpy joins a shipping business. Not the type of shipping she believed it to be, but she tries anyway.

Funny and cute romantic comedy for the most part.

Fixing Up Miss Smartypants by Arkensaw Pinkerton

I hate the "comedic misunderstanding" trope: it gets used way too often in my opinion. This fic, however, does it well.

Contains a LOT of different shippings, with a lot of rising tension and a great climax.

Four of Two by Ariamaki  

I really like this one, for a lot of different reasons. Mature rating, but nothing too explicit.

Comedy:

The Best Night Ever by Capn_Chryssalid

Blueblood gets stuck in a time loop, reliving the Gala day after day after day. I dare you to read this without liking the guy at least a bit by the end.

Very nicely done. It has a romance tag, but there is a minimum of shipping involved

The Prince and the Workhorse by fellstorm

Blueblood and Big Macintosh switch bodies while the former is in Ponyville. The only one who knows is Blueblood's manservant.

Mostly lighthearted comedy, but some really serious stuff gets tossed around as well. Contains Romance.

So, you've grown wings by Steel Resolve

Mane 6 turn into alicorns. Everyone is very confused. Then Discord shows up. Fun and well written. Don't take it too seriously.

A Slice of Life by Dawnscroll

Celestia gains too much weight. Gets put through hell to maintain the Royal Figure. Luna watches. And laughs.

Weird and random comedy. not much sense to be had here.

Do Not Serve These Ponies by Thanqol

Random, Chaotic as discord himself and FUN. Lots and lots of fun. The "Lyra human obsession and conspiracy nut" fanon turned up to it's logical extreme.

The Legend Of Star Swirl The Bearded by Blueshift

You're an Earth pony in pre-Windigo Equestria. You're oppressed, starving and depressed. What do you do?

Infiltrate the Unicorn court claiming to be the world's most powerful sorcerer of course!

Incomplete and updates Very Slowly. Still very much worth it.

My Little Pony: Versus Equestria by PseudoFiction

Probably shouldn't be on this list, as I think it actually is kind of popular at the moment.

It's still on here. I just like it that much. HIE Fic, contains lots of Trixie and comedy

Currently on Hiatus, but what there is so far makes a very nice self-contained story.

Why am I Pinkie Pie?! by Hoopy McGee

HIE in an odd way. The protagonist is suddenly a Pink Equine. also, her personality is seeping into his. And nobody believes him/her!

Random comedy tale, with some interesting identity issues.

Adventure:

Head Full of Cotton Candy by TheManWithTwoNames

Discord grows up. He tries to do good, but he just does not get ponies. And they do not get him. Good thing he has a teacher.

One of my favorites: A look at Discord from after he came into being until he gets turned to stone by the princesses. Comedy, adventure and a bit of sadness.

Contraptionology! by Skywriter

If you read the Skin Horse or Narbonic webcomics, that is pretty much what you should expect (same writer): Comedy, action, and lots of Mad Science.

Elementals of Harmony by FanOfMostEverything

A Magic: The Gathering crossover. Do NOT let this scare you off: I never played, I loved it.

Rule based magic, action, comedy, awesome Derpy and Pinkie.

Night Guards by Raugos

The story of Luna's turn to Nightmare Moon, from the perspective of her most trusted guards and friends.

The Moonstone Cup by Cyanide  

Twilight is entered into a magic combat competition by celestia. And she kicks flank. Very well written action, and a good characterisation of our dear panicked librarian.

Substitute Harmony by blayzekohime  

Trixie, Gilda, Pinkie's sisters, Pinkie and Derpy have to take over as the elements of Harmony. While stranded in a different universe.

Also, Celestia gets blown up with dynamite. Dark tag, but nothing too extreme.

The Ballad of Echo the Diamond Dog by Rust

I waited way too long before reading this. HIE, but the guy gets turned into a diamond dog. Then he meets Daring Do. Lots of action, some comedy, very well written.

Project: Sunflower by Hoopy McGee  

Absolutely Grade A Beautiful. Way too few upvotes in my opinion.

Earth is in danger, Human gets sent to equestria as a scout for a possible relocation of humanity.

Very well written characters, huge ethical dilemmas, and the plot makes a lot of sense, bar one or two suspensions of disbelief.

Mendacity by Dromicosuchus  

Bon-Bon is a rogue changeling. Lyra gets kidnapped around the time of the royal wedding.

Great use of celtic mythology, VERY determined main character.

Mirror's Image by Evilpresident

Twilight was a changeling all her life! Even she didn't know! And she will have to take over the hive some day. Now what?

I really like this one: a lot of thought was put into the events surrounding the season 2 final, and how Chrysalis might have pulled it off better.

Lots of angst, from twilight, and just about the entire rest of the cast, but it doesn't get overdone.

Slice of life:

Petriculture by Kwakerjak

Why is Pinkie.. well...Pinkie. And what the hell is a rock farm? Twilight investigates.

Very interesting way of explaining Pinkie's weirdness. Has a sequel which delves into the concept a lot more.

Darkest Before Dawn by Sessalisk

Twilight as a filly studying under Celestia and at the school for gifted unicorns. Very cute story.

A Cup of Joe by The Descendant  

Slightly sad, but very nicely done. A look into the daily life of a donut shop owner with a tragic past

It Takes a Village by determamfidd

Has a romance tag, but does not contain all that much romance. It does have a lot of spike growing up, realizing that he is outgrowing everyone he knows and will likely outlive most of them.

Deals with a lot of the issues you would expect of a dragon living among ponies: What do you do when everyone who meets you for the first time is afraid of you? How do you deal with your own species if you have never known them?

How do you perform everyday tasks with claws that can cut through solid rock?

Hiatus by Vargras

Luna pretty much dissapeared between the summer sun celebration and nightmare night. Hiatus takes a look at Luna's efforts to learn about the changes in pony culture while she was gone.

The Keepers of Discord by Hoopy McGee  

Discord redemption fic mostly. Exept he does not move a muscle. He is a statue after all.

Funny, slightly sad, and well written.

Duties by Denim_Blue

And another "Everybody becomes an alicorn" fiction. This one is a bit more serious though. Equestria goes through some major political changes, the mane 6 struggle to adapt to their new situation.

Also has some great combat scenes.

Interview With a Princess by Hoopy McGee

A guy writes a letter to a fictional? pony princess. Against all expectations, it gets answered. Interviews follow.

Has some hilarous and/or disturbing Alternate Endings.

Dark:

Pony POV Series by Alex Warlorn

Very dark. VERY long. and very much worth the read.

Alternate universe from the start of S2 onwards, taking a very serious look at the effects of Discord messing around with the minds, bodies and personalities of all the ponies he messed with while he was free.

Which is pretty much everyone in the ponyville area.