Dictionaries & Reference-based Resources

Aruku
The best collocation dictionary on the market for English <> Japanese. Inexpensive (just 300 Yen per month / 3,300 Yen yearly). Highly recommend for when you want to know how words/phrases are used in context, or want greater detail than what is provided in a standard dictionary

Jisho
A fantastic free online dictionary built by Japanese-learners, for Japanese learners. I use this when I want a quick reference to look up words

Grammar Guides

Tae Kim’s Grammar Guide
A fantastic alternative ‘textbook’ for Japanese learners, written particularly well for those coming from the English language natively

Imabi
A complete 100% academic guide of A to Z, covering just about anything you would want to know about Japanese, the culture and how that relates to the language

Maggie Sensei
A huge wealth of well-explained lessons on individual grammar and vocabulary concepts, with easy-to-understand explanations & plenty of sample sentences. The author also actively responds to user questions in the comments.

Online News (Reading Content)

CNN Japanese
A good website for intermediate learners, since many articles ‘read like English’ in word-use and phrasing, which I feel makes them easier to digest. (I would guess they are simply translated from the English publication). This make it a good jump-off point for mid-level Japanese learners looking to supplement their reading. Check it out!

Nikkei Shinbun
The ‘Japanese version of Wall Street Journal’ – world news, business and politics. Difficult, and best attempted as an intermediate/advanced learner. Considered by most Japanese people in the business world as the go-to publication.

Hiragana Times
Similar to NHK Easy Japanese, easier news articles with Japanese and English written side-by-side

NHK Easy Japanese
Articles written in easy and simple Japanese – good for those at the beginner level who want to start jumping into reading as much Japanese as they can

Video Content

Animelon
A site where you can easily and efficiently study Japanese by watching Anime w/ Japanese subtitles. Subtitles have a variety of additional options, such as the ability to look up phrases immediately in the video, making learning new words and watching more streamlined and enjoyable

Youtube
This may seem to be an obvious one, but finding Japanese Youtubers you like is a great way to supplement your learning, especially as it will give you a chance to hear more informal speech. Also a much more fun way to study! Not sure where to start? A perennial favorite is Hikakin!
Bonus: a fun way to practice is to do fan subtitles for channels you enjoy.

Apps

Japanese
(Yes, that’s the name!) This is the main dictionary iOS app that I use personally. I like using the list-creation feature to track new words & Kanji. Lot’s of nice features!

Manabi Reader
A favorite Japanese reading app of mine, which allows you do easily read a variety of content from varying sources, with a number of nice features in the app as well. Highly recommend!
(There is an accompanying flashcard app as well, Manabi, which can be useful for studying full sentences as opposed to drilling single words).

WaniKani
This is cited throughout the guide, but I believe this site, with its SRS system and fantastic UI, to be the best and easiest way to learn Kanji. Some of the vocabulary they teach you is not super useful, some key Kanji are not included, and the first few levels can be a bit slow, but this still remains my #1 recommendation to new learners of the language.
There are a few great fan-made iOS apps as well that can be found with a quick search.

Books

Reading books in Japanese in general is a great way to accelerate your learning – if you can make it to Japan, swing by one of the many Book-Offs, and pick up yourself a stack of cheap reads!

Some specific recommendations I have:
Slang Japanese
A bit outdated, but will give you a good introduction to the lowest-end of formality in Japanese (which you won’t typically get out of a textbook)

Writing Japanese Emails
The only other major book on writing formal Japanese emails I’ve found – a good supplement to the content on this site!

Flo Flo
(Online book site!) A site that uses a similar SRS method to WaniKani, wherein words are tested based upon readings you complete on the site.