Mane Six:

 

Twilight Sparkle:

Afro-German, with Japanese blood * Female * Straight, with exceptions.

Pinkie Pie:

I'm debating rather to make her Native American or Native Hawaiin, but she'd defiantly have Caribbean [Bahamian or Jamaican, or maybe a mix of both] and Swedish heritage. Lesbian, with exceptions.
She's also a trans girl, post-estrogen and post-op.

Applejack:

Afro-American, of the southern variation.

Rainbow Dash:

Mestizo Mexican, with Cuban and Dominican Republic heritage.

Rarity:

Biracial [Egyptian Arab/Sudanese].

Fluttershy:

French,

Octavia only lets one pony refer to her as "Tavi"- Vinyl Scratch. She loves it when Vinyl does it, but she'll punch anyone else who uses that nickname.

Twilight Sparkle gets nosebleeds. Yes, THAT kind of nosebleeds. It always ruins romantic moments for her.

Rarity loves playing the violin, and is also a huge Sam Smith fan.

Don't get me wrong, I still think Twilight loves her male and female friends equally, but there's one headcanon I just need to get out:
She loves masculine culture. Beer, assertiveness, sports, and she evens cross-dresses occasionally.
It used to be her biggest secret, but she's lighted up a bit after seeing how open Rainbow Dash and Applejack were about their expression.

Even though Rarity actually does have a bit of Italian-French blood, her friends still tease her for being a "French wannabe".

I see a lot of people ship Rarity and Applejack as a romantic couple, which is fine, but I personally imagine them having the strongest friendship of the group.

Mane six human body types GO:

Twilight is "average sized", in terms of both height and weight.

Pinkie Pie is, of course, short and chubby; and being a trans woman, has some muscle.

Applejack is on the taller side and muscular.

Rainbow Dash is average height, if not on the shorter side.

Rarity is taller than Pinkie, but shorter than Twilight. Has a thick figure.

I don't care if this is over-used, I still imagine Fluttershy as tall, and has some pudge. She's really insecure about her body.

So in order from shortest to tallest: Pinkie Pie, Rainbow Dash, Rarity, Twilight, Applejack, and Fluttershy.

Oh yeah, and they've all got a nice ass.

Twilight's OOC behavior in "Look Before You Sleep" was because she has (or at least had) a crush on Applejack.

Derpy headcanons:
Derpy's birth name is actually "Dizty Doo". It's mostly used by people who don't know her well.
She isn't as "dumb" as people think. Just bubbly and clumsy.

Derpy's only disability is that she's visually impaired. Her kluzitness, deep voice, airheadness, etc, is just who she .

More relationship headcanons:
Applejack developed a huge crush on Rarity over time, but the feeling unfourtnately wasn't mutual.

Rarity's is Pinkie Pie's Heterosexual Life Partner.

Human Headcanons GO:

Twilight and Shining Armor:

I actually have several headcanons..... 1, is that Twilight's family are Indian, with Asian [Korean] blood, since Twilight Velvet is mixed.
The Korean part doesn't really show through Shining, but it does through Twilight Sparkle.

2. Twilight is a black American.

3. She's a full-blown East Asian, probably Korean.

And finally, 4. one where's she's a mix of the two above.

The Pie Family:

1. Mixed Race. Caribbean-American [Jamaican-Bahamian mix] on their Dad's side and Swedish on their Mom's. For most of the sisters, it's obvious that they're biracial, with the exception of Maud, who can easily be mistaken as a full-blown PoC.

2. Pinkie's Native Hawaiian, with African blood.

3. Pinkie Pie's biracial [Native American/African]

The Apple Family:
Ohh boy..
Applejack and her immediate family are African-American, of the Southerner variation.
Babs is part black, part white-Italian, and probably light-skinned.
Braeburn is partly Scot-Irish American.

Rainbow Dash:
1. Latina. Mom's Cuban, Dad's Domincian Republic, and one of her Grandparents were Mexican.

2. Rainbow Dash is biracial [part Latina, part Afro-Hispanic], probably with the same principles above.

Rarity and Sweetie Belle:
Rarity and Sweetie Belle are multi-ethinic: Part Sudanese-British, part Egyptian Arab. The former on their Mom's side, the latter on their Dad's. Rarity has a nice phyisical mix of all of her backgrounds, but Sweetie Belle could be Egyptian passing if it wasn't for her (or his, in keeping with my headcanon) curly hair. Oh, and they have a bit of Italian-French blood, which is fine with Rarity, since she will always adore French culture.

Fluttershy:
My most prominent one is that she's mostly Apsaalooke Native American, but partly Japanese-Chinese and French-Canadian. They all show.

Another one is that she's Japanese.

Or Persian.

Princess Luna will always love elegant, old-fashioned dresses.

Religion headcanons:

Twilight Sparkle is Hindu.

Pinkie Pie grew up Amish and is non-religious, though not necessarily an atheist.

Applejack is a Protestant Christian.

Rainbow Dash is either non-religious or atheist.

Rarity is Islamic.

Flutters is Catholic.

Religion headcanons:

 

Twilight Sparkle is Hindu.

Pinkie Pie grew up Amish and is non-religious, though not necessarily an atheist.

Applejack is a Protestant Christian.

Rainbow Dash is either non-religious or atheist.

Rarity is Islamic.

Flutters is Catholic.

Applejack's parents went to-ahem-the store.

Gender Confused!Twilight becoming depressed after being labeled as a "princess."

Random stuff:

I have two headcanons for the clothes Twily wears: One, where she almost always dresses boyishly- sweater vest, tie, pants. Two, where she dresses like a stereotypical business woman.

Fluttershy always dresses modestly.

"A Lotta Love"" is Princess Cadance's favorite song.

Hairstyles of the mane six:

 

Twilight Sparkle:

Sleek, thick black hair, which she occasionally wears in a bun. Has clip-on hair extensions representing her pink and light purple streaks, but probably finds them embarrassing, and only wears them on special occasions/when she's feeling happy.

 

Applejack:

Typical blonde beauty. Really likes ponytails since she can wear them while working.

 

Fluttershy:

Dyed hair pink, was naturally light brown. Despite wanting to love herself and her choices, she's still really embarrassed when she gets attention for it out in public.

 

Pinkie Pie:

Has the thickest, bouncy, curliest hair all over the place, and loves it! She'll go wild with all sorts of dye, but unlike Fluttershy, couldn't care less about what others think.

Rarity:

Wears the hijab most of the time, but when she's not, she'll usually put it in a sophisticated bun or ponytail.

 

Rainbow Dash:

Brownish-black hair. Has all sorts of colors dyed in.

More humanized background/fan made pony headcanons:

Raindrops is Japanese.

Daisy is from the US, Lily is Native Hawaiian, and Roseluck is part white (Canadian), part Romani. They're in polyamorous relationships with each other.

Button Mash is biracial [black American/white], with his Mom being a white South African.