This is a list of resources that I have found helpful in my study of Japanese. I hope some of them will be of use to you as well.

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Ayamel
http://ayamel.byu.edu

This a very powerful video viewing platform developed by the ARCLITE lab at Brigham Young University. Ayamel allows you to interact with subtitles and so better learn words and match what you hear with what you see.

Onomato Project
http://onomatoproject.com/

This is a great place to practice your Japanese Onomatopoeia 擬音語 (ぎおんご) and 擬態語 (ぎたいご) 

Nekodanka DailyMotion Channel
http://www.dailymotion.com/nekodanka

This channel has a lot of old animated Japanese folktales that are great for Intermediate to Advanced listening practice.

My Kikitori
http://mykikitori.com

This is a great beginning level listening practice website.

DLI Online Lessons
​https://gloss.dliflc.edu

The Defense Language Institute has a database of many free lessons that you can go through for many languages. Simply select Japanese and search based on your desired criteria and availability.

Japanese Go
​http://japanesego.com

This is a good collection of free Japanese listening practice videos and clips. Some even come with a script.