Vocaloid and Pokemon resources can be found on the relevant pages.
Learn Japanese
kitsunekko - Japanese subtitles for anime (English subtitles available as well)
Anki - Flashcards
Creative Projects
The Spriter's Resource - Assets from various games
Games
Reading
HDoujin Downloader - Download manga galleries from various websites
Fichub - Download fanfiction from various sites (such as FFNet)
Writing
Onelook thesaurus - Thesaurus with a thorough filtering system
3ds CFW
PSVita CFW
Other
Image to PDF - Exactly what it sounds like. I personally use this with HDoujin Downloader.
MP3Tag - MP3 tag editor
Yu-Gi-Oh ship search - Search for ship names from DM-Sevens by their components
