I've been studying Japanese for around a year and a half now. While I don't think anyone has a strong definition of the differences between beginner, intermediate, advanced, etc. levels of Japanese, I'd guess I'm around advanced beginner to low intermediate. I imagine I'm going rather slowly, compared to many people, but on the other hand, I'm still chugging away at 18+ months.
In particular, my reading level is around low intermediate, while my listening is maybe beginner to advanced beginner at best. Being a self-learner, I haven't really had much in way of speaking practice, so in that regard I'm pretty much a full beginner.
In terms of actual statistics, I've learned around 1,100 kanji and 4,500 words .
Tools I've Used
The most intimidating part about learning Japanese to me (and I suspect, most people,) is the writing system--specifically, the kanji. Sure, learning hiragana and katakana is more difficult than just using (mostly) the same alphabet, if not the exact same sounds, to learn Spanish or another western European language, but in the grand scheme of language learning, picking up fewer than 100 relatively simple characters isn't a ridiculous time investment.
Kanji, however, is another story. Your need to learn thousands of characters (2100+ for just the basic Jouyou kanji.) Many--or most--of the characters are complex, and often look similar. It takes time and dedication, and the huge number of things to learn can be overwhelming. When I started learning Japanese, the thing I dreaded most was having to memorize kanji.
Wanikani uses a spaced repetition system (SRS) and mnemonics to help you learn kanji in a way that really sticks. It breaks each kanji down into one or (usually) more parts it calls "radicals" and uses those radicals to create the mnemonics that help you remember the meaning and reading of each kanji.
Right now, I've just started level 34 out of 60--or slightly more than half way done.
Wanikani is subscription-based, but the first three levels are available as a free trial.
Before Wanikani, I used Anki for my SRS. It was okay, but I fell in love with Wanikani's interface and SRS system. Houhou is an SRS application that mimics a lot of what Wanikani does in terms of interface, and can easily be changed to even use a very similar SRS level system (and with a little work, even a practically identical one.)
This is what I've used to learn vocabulary outside of Wanikani. All of my non-kanji vocabulary goes in here, along with plenty of kanji vocab I encounter in the wild (that is, outside of Wanikani.)
Houhou allows you to look up and add both kanji and vocab from directly within Houhou, though it does not include any sort of mnemonics--it's a pure SRS system. I plan to use it to learn kanji outside those taught by Wanikani, but I haven't got to that point yet.
Houhou is Windows-only, so that's a little unfortunate.
Textfugu, also by the people at Tofugu, is a beginner-level Japanese textbook.
This is actually where I began learning Japanese. It starts at the complete-newbie level. It will teach you hiragana, katakana, some vocab, basic particles and conjugations.
It also starts to teach some kanji, though that is redundant with and inferior in both method and quantity to Wanikani.
Textfugu hasn't been updated in a long time, and doesn't teach that much--it's a great foundation, but not much more, and considering it costs money, I have a hard time recommending it. Though, if you have a lifetime membership, you get a discount to Wanikani (monthly and yearly subscriptions only) and a few other sites.
This online textbook is a good base, in my experience. I've seen plenty of people complain about it. Maybe those criticisms are correct, and maybe they're not--I don't think I'm even close to the level needed to really evaluate it to that extent. 
What I do know is the sort of no-fluff way he covers a lot of grammar points really helped them stick in my head in a way they didn't necessarily when I read about them in Textfugu or Genki.
The online version is completely free, though I personally bought the paperback version of the book because I find I learn better from dead tree books, for whatever reason.
This amazing book is by far my favorite among the textbooks I've tried.
It starts out with the the most basic grammar points possible and works up through tons of particles, conjugations and other grammar. The book uses panels from manga--generally slice-of-life or gag type manga--along with an explanation of the context leading up to the example in order to illustrate the grammar point it's teaching you.
I love this book. It's taught me so much that has really stuck with me. It's easy to read because, while the explanations are textbook-like (as they should be), the examples are taken from actually Japanese-language media, which gives them a much more memorable quality, compared the the contrived sentences every other textbook uses.
That's my Japanese learning stack so far. Besides those dedicated resources, I'm also learning by reading native Japanese material--some games, some manga and some (very low-level) literature. That's where I pick up most my vocab outside of Wanikani.
I also have a few other resources I want to touch on. Some of them I use, but that I probably don't really get much out of, and others I just didn't like much. In both cases, someone else may find them more useful, though, so I want to talk about them--look for those lists in a future post.
|||"Learned," here, means I have those kanji and vocabulary at at least the Guru level on Wanikani or equivalent.|
|||The radicals Wanikani uses are not the same radicals used, e.g., for dictionary look up of kanji. Even for those where the actual character itself is the same, Wanikani often uses different names so it can more easily build mnemonics.|
|||Most (maybe even all) of the criticism I've seen has been about the opinions expressed by the author, rather than the technical aspects he covers.|