Following is a list of Japanese Language Learning Tools that I’ve found helpful for studying Japanese:

Flashcard (SRS) tools:

• Anki (pc, web, mobile) is the primary study tool of choice for most language learners that I am aware of. It is free on every platform except iOS($25) and has many customization options, study statistics, and copious pre-made flashcards.
• Repetitions is a SRS flashcard app which comes loaded with a kana deck.  I have used the app, but not the deck.  Basically a dumbed down version of anki, but if you want to use SRS on your iOS device for free, give this one a try.  Otherwise, I’d recommend Anki.

Step 1 (Kana) Tools:

• An Anki deck for learning Hiragana and Katakana.  If you plan on using Anki to study, why not get started right away with this deck!
• Remembering the Kana is a book by James Heisig, the same author as the popular “Remembering the Kanji” and uses a similar approach.
• Remembering the Kana is a video series by a fellow learner based on the Remembering the Kana book.  I have not watched it, but I am familiar with the creator, so I am sure that they are worthwhile.

Step 2 (Vocab & Kanji) Tools:

• Core 6K is the anki deck that I’m using.  It’s basically 6000 Japanese sentences translated into English.  What makes it popular with Japanese learners is that each card has vocab in kanji, kana and english and the sentence in kanji, kana and english.  There are also native spoken audio files of the sentences that you can load.  All of this lets you remix the material to learn vocab, kanji, listening comprehension, pronounciation… all with the same words.  There are other decks with slight modifications.  If I had to start again, I might try this deck instead.  See the step 2a page for a more comprehensive explanation of core 6k and how I use it.
• Remembering the Kanji is the most popular textbook for learning to read and write Japanese characters.  Each kanji is paired with an english keyword and also a “story” to help you remember the keyword.  The book starts with simple primitives (radicals) which make up a kanji charactor and then progressively “builds” new kanji from previously learned radicals and kanji.
• RTK 6th With Stories is the Anki deck that I’m using to learn my Kanji.

Step 3 (Sentence) Tools:

• Tae Kim’s Guide to Japanese is a website, book, and app that covers essential Japanese grammar.

Step 4 & 5 (Real Japanese) Tools:

• Subs2srs (pc) allows you to create anki audio flashcards from Japanese dramas and movies. This allows you to study colloquial Japanese as it is spoken in “the wild” by Natives instead of sanitized Japanese spoken on learning CDs.
• Rikaisama(web) is a browser add-on that pops up a definition of words that you hover over.  This makes it easy to read native Japanese text and add unknown words to Anki.
• Yomichan is a Rikaichan like application that allows you read Japanese and click to add words directly to anki.
• Morph Man is an anki plug-in that knows what words you know and optimizes the order of new cards for the words that you don’t know.
• Epwing2Anki is an application that creates anki vocabulary & sentence cards from a word list.
• Japanese Text Analysis Tool can be used to create word lists from arbitrary Japanese text that are sorted by frequency.
• Wordlist Duplicate remover Finds both unique and duplicate words based on a list of words that you want to learn and the words already in your Anki deck.