The Thessalonica Legacy - the best first contact scene I had the pleasure to read. This coupled with an expertly written adventure makes this gem truly unique
The Colour You Bleed - nice, deep psychological study of changing one's views after a traumatic event. It's also a good story
My Second Life - [MATURE] the best human in Equestria adventure story. The saucy fragments are cleanly marked but I suggest reading them as they enrich the story
The Book of Friendship - [mature, !*HEAVY GRIMDARK*!] - a stunningly good story about working against impossible odds with a touch of comedy. The heavy grimdark stuff is only in one chapter, after which the story gets a bit lighter
Past Sins - one of the greatest stories ever written here. A true classic that's deep but, at the same time, manages to perfectly strike a balance between happiness and sadness. Does *NOT* contain any grimdark or excessive violence.

Whiplash - an adventure story with a very nice psychological twist
Two's Company - Three's a Crowd - an expertly written, positive story. If you need something light after a heavy grimdark, this is the one to get. It's not a comedy per se, it's a very light, warm story, with an interesting plot that's just a great joy to read. The clop scene is also worth mentioning as it is the only one I am aware of that deserves an "everyone" rating while still getting the message across :). In short: a great, safe-for-work story!

You will notice that the last 2 slots are empty. I could have easily filled them with some very good stories, but this list is for the best of the best gems out there. Before a story is put into this hall of eternal fame I always think very hard if it really deserves to be put here.

There is one story which will probably help to get slot #9 filled. I just finished it and... I LOVED THIS GEM. I will probably decide within a week if the story is worthy of this highest merit a single reader can give to a Writer.

Ladies and Gentlecolts! We have yet another, even more serious contender: Falling Stars by Rokas. This looks like a superb addition to the Thessalonica Legacy and I think that's enough for a praise. If it continues to deliver such a fantastic quality, it will be in my Top 5 easily.

Another of those "I need to think about" gems: What Princesses Need by Aegis Shield. Something like a Freudian Slip only much, much deeper. FANTASTIC gem! After a few weeks I will most probably move it into the Top 5... It's that good! As a rule I never add a story without watching it for a few weeks.

Now the thing I've never ever thought I will ever put here - a clopfic: Xenophilia - sex, NSFW, mature, Human in Equestria. Author: AnonAuthor; story posted under AnonponyDASHIE. This is a FANTASTIC story, even without all the saucy content. This gem avoids the vulgarity of 99.9% of all the clopfics, while at the same time being monitor-melting hot. The Writer (with a capital 'W') managed to build a believable world that takes a lot from the show, remains as close to it as possible and adds to it a lot of interesting, new elements. This story is a true gem that any adult should take a look at. Even if you hate clop posted on fimfiction due to a poor execution, give this one a chance!

I've found yet another [NSFW, SEX] story that really puts storytelling to new heights - An Escort's Journal by MagusMeister.
The story is about a pony escort (i.e. prostitute) life, with all ups and downs. Yes, the sex is there, but the story strong points is the first-class storytelling and not clop.

Maidens Day [NSFW,SEX] by bookplayer. This one is a giant world-building behemoth! Each paragraph is an excuse for making the Author's version of the MLP world more interesting and genuinely original.

Finally, we have a very novel idea for a HiE fic: Oh to be Old Again. This breathtakingly good gem is truly fascinating as Minalkra managed to build a highly believable word that takes a lot from the show but, at the same time, adds enough new elements to be interesting (Yes, I know I wrote the same thing about Xenophilia :). I think this story is a spiritual, no-clop version of it - very different but still a bit similar - and that's a good thing!). What's more, the main character of the story is an ordinary guy - no superhero, no superhuman powers etc. I really do recommend this story, even if you don't like HiE that much.

Without a Hive - this one has true POTENTIAL. So far it's only 3 chapters long but... it ROCKS! The story is a fresh look at changelings from their perspective - treating ponies as a source of food but, at the same time showing emotions that only a real changeling could feel. Highly recommended, especially if you want a truly unique experience.

Do you want to have a good laugh? If you do, read Even Stranger by SaltyJustice. This gem is for me the best comedy story about Changelings. Thorax, a young changeling, becomes a super-secret secret agent (think Agent 007, ugh, I mean Agent Triple-Zero). Hiliarity ensures! Caution: I won't be held responsible for all drinks you will spit out or the state of your clothes after a prolonged ROTFL while reading this story.

Derplicity - another great comedy story. This one is actually a bit more serious than Even Stranger but it's still really funny. It's writing is absolutely top notch!

Your Human and you- if you loved A Voice among the Strangersor Chains or you will adore this one. A magnificent beginning that develops into a fantastic story. This time, it's a complete role reversal - humans are unintelligent beasts that are bred by ponies. Except that one of the livestock is not from Equestria .
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Cultural Artifacts. One of very few Human in Equestria stories that focus on cultural differences. What really makes this gem unique is that the language barrier is depicted flawlessly. This is one of the most realistic HiE story I've ever read. With the greatest of sadness I have to say that I have changed my mind. The beginning is FANTASTIC but unfortunately the later chapters don't make any sense for me and are a chore to read. I will cherish the memories I had while reading the first chapters of this story but I really cannot recommend it anymore. I gave it a chance, left a comment to the author but unfortunately he/she decided not to change anything and continue the all-nonsense approach. I recommend checking the comments out first before reading this story.
This is a really sad day for me to include the story I once loved so much to the ones that simply don't click anymore. STAY AWAY.....