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Nihongo Overlapping

On this site, you can practice your pronunciation using a method called overlapping, where you speak along with the model voice, while looking at the script. After you practice, you can listen to and visually check your pronunciation.
やってみよう日本語クイズ(Let's try Japanese quiz games.)

Learn intransitive verbs, transitive verbs, and onomatopoeia through quiz games.
Fun Trivia Quizzes - Japanese

Here you can try quizzes on kanji or other aspects of Japanese.
Rikai.com

This is a reading support tool which shows you how to read - and the meaning of - Japanese words that use kanji.
This is Japanese! [Intermediate] From Self-Introduction to Debating Current Affairs

Meiji University developed this site for intermediate and pre-advanced learners to practice speaking and listening. They used the study books, Nihongo de Chosen (Challenge in Japanese)! Speech & Discussion and Motto Nihongo de Chosen (More Challenge in Intermediate Japanese)! Speech & Discussion for reference.
HiNative

This is a language learning Q&A site where you can ask and answer questions with native speakers of more than 170 countries.
RomajiDesu

This is a site that uses Jim Breen’s Japanese Dictionary and his Kanji Dictionary to create an online dictionary site that also lets you convert romaji into hiragana and katakana.
Origami Club

This site introduces lots of drawings and animations for how to fold various origami shapes.
福娘童話集 Hukumusume Fairy Tale Collection

This is a website where you can hear traditional folk tales, legends and fairy stories - from Japan and all around the world - read aloud for you in Japanese.
Visualizing Japanese Grammar

Here you can check your understanding of the main points of beginner-level Japanese grammar, through watching, listening and reading.
United Links for Japanese Learning Web Resources

This is a convenient collection of links to Japanese-study websites that allows you to choose the site you want to visit by selecting various categories, such as Japanese ability-level, display language and skills covered.
Genki Japan

Using this site you can study Japanese in an easy and fun way and find out some basic information about Japan. There's plenty of games and songs to be found here too.
Japanese Kanji Map

This site is part of Rikai.com. For kanji you are interested in, you're shown 6 examples of how different characters can go before or after them to make various 2-kanji compound words.
Tokyo Metropolitan University mic-J AV Resources for Japanese Language Instruction

An audio-visual resource site designed by Tokyo Metropolitan University. There is an abundance of YouTube content, useful as well for those who study alone.
Japanese Typing Practice for Beginners

You can use this site to practise typing hiragana, katakana and kanji. There is also some sentence-level practice and dictation practice.
NHK for school 歴史にドキリ(History is Amazing)

An NHK site made for Japanese 6th graders to learn about the history of Japan. Ideal for advanced learners of Japanese to study listening and reading comprehension.
Cultural Digital Library

Enjoy looking at photos and videos as you learn about various traditional Japanese performing arts such as Kabuki and Nohgaku.This site is operated by the Japan Arts Council.
NHK やさしいことばニュース NHK NEWS WEB EASY

Here you can read and listen to easy-to-understand Japanese news.
にじいろ（Nijiiro）

This is a website that provides information to those who want to study in Japan and those who are currently studying in Japan.
NHK WORLD-JAPAN やさしい日本語 | Easy Japanese Conversation lessons

This website was created in conjunction with the NHK World-Japan radio program (supervised by the Japan Foundation Japanese International Center). Enjoy learning phrases and grammar useful for traveling in Japan while watching anime and videos. This site is offered in 21 languages.