Japan

Japan is a country in Eastern Asia.

Osharena manga
Milky and Pinky were seen speaking Japanese.

Friendship is Magic
The Mane Six took a trip to Japan. Poniko and Roku-chan are from Japan.

Friendship is Magic Pucchigumi manga
Several ponies were capable of speaking Japanese.

Little Pony TV
Mimorin is from Japan. The Ponyville TV Station was able to communicate to Amakuchi HKT48, a Japanese band.

Equestria Girls
While never explicitly appearing, Micro Chips referenced Japanese culture when he wondered if had a samurai sword.

In our world
My Little Pony: Friendship is Magic was relatively popular in Japan but was canceled after a few seasons. The voice cast for Friendship is Magic and Equestria Girls was quite expansive with many talented and (presumably) famous voice actors, most of which had big roles in popular anime from the 90s and 2000s.

People and production

 * People in general (voice actors, writers, artists, notable fans, etc)
 * Voice actors

Takara toys
In the 80s, Takara produced a handful of My Little Pony toys, with original characters.
 * Ami Ami
 * Sara Sara
 * Kuru Kuru
 * Fuwa Fuwa
 * Pinky
 * Milky
 * Lily
 * Popo

Regional media

 * Osharena manga
 * My Little Pony (Pucchigumi manga)
 * ShiーRudeasobō! Mairitoruponi
 * Equestria Girls (Phase 6)
 * My Little Pony The BOOK (Phase 6 manga)

Cultural references
As manga and anime have grown in popularity in recent years, there have been a handful of references to Japanese media.
 * Luna Eclipsed features ponies dressed as Usagi Tsukino and Makoto Kino
 * features a cameo by Usagi Tsukino and Makoto Kino.
 * The Nightmare Rarity arc also features "Shadowforces", creatures who may be based off of the legend of the Moon Rabbit.
 * features artwork of various anime characters such as Usagi Tsukino, Bulma Briefs and Rei Ayanami.
 * features artowrk from Attack on Titan.
 * features panels drawn in a manga-esque style and a theater known as "Kazumi Theater, or "Beautiful Theater"
 * Queen of Clubs features the Anime club, a club of people who enjoy anime and do henshin/senshi poses