From Fimfiction's own FAQ

Main Tags

Why you can't have (and shouldn't want) more than six categories (main tags)

Categories are designed to be broad descriptors of a story's content or themes; they're designed in such a way that no more than six should be required at any time, and in fact, some of them conflict and cannot be used together (see the section on 'category conflicts). For this reason, we ask that you restrict your story to 6 categories - any more than that and you probably need to reconsider what your story is about, and find the best way to express which ideas and moods are central to the story you're trying to tell.

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Tags: main descriptions

Categories are thematic tags for all stories. What this means is that each category selected for a fanfic should represent predominant themes throughout said story. Any piece of writing can have all elements listed below on differing degrees, but it is not necessary to choose all categories that your story is going to have just because they appear in it; you should simply choose the categories that best describe your story.

Romance: A story that has a predominant romantic theme, or explores a romantic relationship (innocent or intimate) between characters.

Exception: Having two characters already in a relationship as part of the story, simply as a couple that appears but whose relationship is not explored in the least, does not merit the category being tagged.

Example: Twilight's List by Kits

Sad: The sad category can be a little bit confusing. Choose this category for stories that are designed to evoke sadness from your reader throughout the story. This is a main theme for your story; maybe the character suffers from depression, or it deals with the aftermath of a dear friend's death (remember: that doesn't make this a tragedy). A sad story can end in a happy note.

Example: Never a Rainbow by Norsepony

Tragedy: The most confusing category by far, the Tragedy Category is often misunderstood and misused. A Tragedy has, by definition, a sad ending, but it doesn't mean the story is sad until that point; unlike a Sad story, it always, always will have a sad or bittersweet ending.

In a Tragedy, the heroine fights through amazing odds to achieve her objective, and just as she's about to get there, she fails through her own folly, or perhaps because she cannot fight fate in the end after all. Ultimately the hero fails; their friend dies; the world ends... our hero dies. Any outcome, as long as it involves the hero's failure in their struggle and the bitter result of it is what makes a Tragedy... a Tragedy.

Example: Gift by Shortskirtsandexplosions

Dark: If you boil it down, a Dark Category story brings forth the contrast of good and evil. The story deals with corruption, war, death (violent), horror... basically what would make a world 'darker and grittier'. It doesn't have to be outright violent, for example, if you look at most fairy-tales they have a lot of happy or even nice things happen before the ultimate dark aspect (the death/torture/destruction of the bad guy or unfortunate hero) takes place.

Example: Backwards Through the Mirror by Rusty the Brave

Comedy: A story whose purpose is to make the reader laugh. It might sound easy, but it isn't as simple as it seems. In any case, if your story centers around shenanigans and funny happenings to your characters be it by circumstance or their own actions this is the category for it. Comedy can be circumstantial or even seem serious at times; Jonathan Swift's Gulliver's Travels, for example can be pretty hilarious if you know the context of all the things he's criticizing in it.

Example: Contraptionology! by Skywriter

Random: A random-tagged story will contain major elements in storytelling that reflect a lack of logic in how they came to be.

Example: Twi Hard 2: Twi Harder by Arcainum

Adventure: An adventure story is focused on a grand or even epic quest of some sort that the characters take part in. Although this doesn't strictly have to take the form of the aforementioned quest format, it does involve events that affect more than the life of a few ponies or characters. This will usually affect whole towns, cities, even the world and usually involves a major catastrophe that can be averted by our heroes either by stopping the villain or doing something else to diffuse the situation.

In-show references would include: Friendship is Magic (Nightmare Moon); The Return of Harmony (Discord); A Canterlot Wedding (Queen Chrysalis); The Crystal Empire (King Sombra). Notice how all the mentioned episodes affect the entire world in some way or other.

Example: The Flight of the Alicorn by Ponydora Prancypants

Slice of Life: A Slice of Life story is a simple, few-characters-affected story. It can be a minor adventure, like a trip to Canterlot, or an encounter with a changeling, or even a simple quest but again, its objective is to highlight a moment in life for a character or group of characters; it is not intended for world-altering events.

It is usually more character-centric and might involve a deeper look into a character's motives, their achievements and what makes them change for better or worse.

Example: Life is a Lemon by Blueshift

Crossover: A crossover story is when two different 'worlds' (read: sources) collide. If you mix MLP with any other cartoon, book, anime, show, radio program or whatever... it is a crossover. This includes 'amalgamations' of worlds, such as Fallout and MLP.

Examples: Any Fallout: Equestria story is a crossover; My Little Denarians by Chengar Qordath; SKYGUN by MytrhilMoth

Alternate Universe: Stories wherein the ponies are in an Alternate Universe as defined as not based in the Canon universe of the series: Alternative worlds, parallel universes and such. (Not Crossovers, unless it's a crossover with an already-alternate universe)

An Alternate Universe story has deviated from the basic setting of MLP: FIM in some way or another: much more heavily steam-punk; Nightmare Moon/Discord/Sombra/Chrysalis won scenarios and so forth.

Example: Harpflank and Sweets by Arcainum; Night's Favoured Child by Municipal Engines

Human: A human visits Equestria. Or the ponies are turned into humans. Or they were always humans and so on and so forth. This tag is not required with Crossovers.

Example: WD: The HiE Experiment by Wanderer D; Anthropology by JasonTheHuman

Anthro: Characters are anthropomorphised (standing on 2 legs, hands instead of hooves, etc)

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Why do certain tags conflict?

Adventure and Slice of Life

Given that an Adventure involves going completely out of your daily life (even by Ponyville standards) it completely takes precedence over the Slice of Life, which can only happen in day-to-day experiences. Defeating Discord is not a day-to-day experience, even if characters can change or grow while that's happening.

Comedy and Sad

Sometimes people get confused and think that morbid humor is equal to a sad comedy. It isn't. You cannot have sadness in equal measure to comedy in a story. One will take the spotlight, because in the end your story will achieve primarily one outcome: either it makes someone sad... or it makes them smile.

Ratings Tags

While the idea of 'maturity' is a difficult one to properly define, for the purpose of stories on Fimfic, the detail of a story's maturity level lies in the description and events contained therein. 'Teen' is anything more risque or salacious than content you might see in the show - overt shipping, foul language, minor violence with cursory descriptions, physical affection more intense than a quick peck on the lips - where 'mature' is anything that should require an aged or mature perspective to read; things like extreme violence, explicit descriptions of physical intimacy, or content intended for older audiences.

This is an answer that's difficult to pin down, so here's a quick guide to follow: 'Everyone' = content that would be acceptable in the show, with some bending for things like alluded shipping or very light affection, 'Teen' = content that is more mature than the stuff that appears on the show but doesn't push the envelope too far (light foul language, some romantic description), 'Mature' is anything that involves material that would require an 'adult supervision' recommendation on a tv broadcast (sex, extreme violence, etc). Just use your best discretion, and feel free to PM a mod if you have a question about the specific content of your story. At worst, you can always submit and be told that a change is required if the maturity tag you've selected doesn't match the discretion of the story-approval team.

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Additional Tags - Gore/Sex
This is simple enough: use 'gore' when there is explicit description of violence/grotesque imagery in your story, and use 'sex' when there's... well... sex. On a Teen rated story, 'sex' can be used to indicate sexual humor or situations that are heated but don't have explicit sex.

Character Tags

Character tags on stories are largely in place for readers, and not for authors. While you might have a great deal of characters in your story, the character tags are intended to make it easy for people to search for stories that feature one or more characters in a prominent role within the narrative. For this reason, we have a limit of 5 character tags per story, as the notion of focusing on any more characters than this as key players in the story is not really tenable. If you feel your story is an exception, we would ask that you consider ranking your character tags in order of significance, and try to apply the ones that would best correspond to reader interest in your story.

Some of my own thoughts on the matter:

Main Categories
Sad/Dark/Tragedy:
While often lumped together, these are three distinct things.

Tragedy in particular can be confusing to new writers. Tragedy doesn't refer to the word "tragic" as in bad or sad things happening. It is a literary term that is diametrically opposed to the literary comedy. Both of these literary terms refer to the end of your story. If everyone lives happily ever after, your story is a dramatic comedy. If the protagonist finds his beloved dead from suicide and thrusts a dagger into her own heart to join him, as in Romeo and Juliette, then your story is a dramatic tragedy. Both stories could look completely identical up til the climax.

What most people tag as tragedy really is just sad. Sad stories deal with the overall theme of your story. While there may be a happy ending, if you intend your readers to have a box of tissues handy, this is your tag. It could be anywhere from "my friend/familymember died" to "I learned there is no Santa."

Dark, like Sad, refers to the overall theme of the story. A sad story about the death of a parent isn't necessarily Dark. It becomes so when you explore the grim details of how cancer destroyed their health, and the family had to struggle with medical bills, hearltess insurence companies, aggressive bill collectors, and loan sharks.

Comedy/Random

Another common mishap happens between these two tags. Being random is often an attempt at being funny, but a story can easily be one without being the other.

Adventure/Slice of Life/Neither

The category conflict section of the FAQ helps clear up why you should never have both of these tags, but the descriptions seem to imply one or the other would be appropriate to all stories; this just isn't accurate at all.

Remember that you ideally want as few tags as possible on your story. Tag only if it seems especially relevant. If your story is some grande quest assigned by Princess Celestia herself and will save Equestria from the big bad, by all means mark it as an adventure. If your story is about this really neat idea you had about how Snails gets up before dawn to make it to class on time, because of how slow he walks, and the neat things he sees in the still-sleeping Ponyville, Slice of Life seems appropriate because you're focusing on a piece of day to day life.

By contrast, you could be writing about how the two members of your OTP realize their feelings, confess, and explore their budding new relationship. While this is certainly within the scope of Slice of Life, the fact that the story is centered around a Romance should take precident. Use the SoL and Adventure tags sparingly, mostly when other categories don't fit better.

Romance

As pointed out in the exception in the FAQ, just because you have two (or more) ponies in a relationship, being lovey-dovey with each other, and so on does not mean you should add the Romance tag. The romance needs to be a major component of the story. Take a look at popular movies/books that are out. They always like to tack on some romantic elements. Your action flic featuring exploding zombies and a pirate ship-chase through the Panama Canal wouldn't be complete without the sexual tension between the protagonist and the henchman of the villain, right? Doesn't make it a romance.

If your story is about either the start of the relationship or focuses on the relationship surviving trials and tribulations, then put that tag on.

Human/Anthro
These tags serve more as a warning to readers than anything else. A lot of people want to read MLP stories because they want to read about ponies. These tags let them know that the writer is messing with the basic aesthetics of the show and a lot of readers don't like that.

Really ask yourself if the human/anthro element of your story is important or not. Does your story gain any value for turning the ponies in it to another bodyform?

Consider that ponies already have human-like traits in the show. A lack of hands doesn't keep them from easily interacting with their environment, they often wear clothes, and they have technology.

These tags, while appropriate for stories where the ponies are really bipedal and/or humans, are probably better saved for stories where ponies meet/interact with human/anthro characters, like your typical HiE story.

That all said, your story can have multiple things going on at once. Still, six tags is an awfully unfocused story. If you're finding yourself using a lot of tags, consider narrowing the focus of your story down. If you just can't decide if the dark or sad tags seem more appropriate, choose Dark.

Character Tags
Just because you have a character speak a line in your story, or present in a single scene, doesn't mean they need to be tagged.

Ask yourself if the plot would change drastically by swapping a particular character out for another.