Below is a list of the educational resources I have used and continue to use. These have all shaped my development in some important way. There are thousands of options out there, some of which may be just as good or better. But these are the ones that really taught me something and have helped me grow as a musician, singer, composer, producer. I'm almost exclusively a self learner. I've not had the best experiences with one on one instruction in the past, and I always came away from the lessons I did take (two different guitar teachers, one piano teacher) thinking I could learn more efficiently and for much cheaper on my own. One huge caveat to this is the quality of instruction I've received from Berklee (see below). I still think that having a great teacher is probably the ultimate way to learn, I've just had bad luck and I grew tired of looking when I had so much information at my disposal. This page will be updated intermittently going forward as I'm always trying out new lessons and instructors. I'm a lesson hoarder, and I hope I never recover.
General Music Education Sites
Berklee Online - if I had to choose one place to learn all I need to learn about music, this would be it. I can't think of a topic related to music that you can't learn here, and the level of instruction and community is the best I have seen, and I've looked in a lot of places. The main drawback is the cost. I don't know that I would have made the leap of faith and paid out of pocket initially, but luckily I have the GI Bill and I now know that I will most likely take more courses even after I've finished my degrees and used up all of GI Bill eligibility. They have a lot of free material on youtube as well as their home pages that can give you a taste of what they have to offer. They also have a lot of good info on youtube.
Macprovideo - after Berklee, I have learned more about music and technology from this site than any other. While it's heavily oriented towards creative arts (Music, Film, Games), there are a wealth of user level technology tutorials on here. There's a bit of everything in here - music theory, software, production, ear training, etc. They go into exhaustive depth on most of the prominent DAWs (Pro Tools, Logic, etc.), and they've been around long enough that there are years of archival tutorials. Even better, they are constantly updating the site with new material. I don't know the frequency, but it seems like there are new tutorials (often 1+ hours or more) every week. They have a broad range of teachers, many of them notable industry professionals. Despite being enrolled full time at Berklee, I've kept a yearly subscription to this site, because there's always something I want to learn or review on here.
Guitar Oriented Sites/Courses
Basic Technique
Troy Stetina's "Speed Mechanics for Lead Guitar" is still the default technical instruction book I would recommend for someone aspiring to become a great rock or metal guitarist. You could spend years learning the lessons in this one book, which can be had for around $15. Probably the best $15 you could spend starting out in rock/metal. He has a wealth of other books on his site as well as most resellers like Amazon.
Theory
First and foremost, it's probably best to take an actual theory course or two before you start pursuing things on your own. Yes, you can do it on your own, and if you're like me, you'll probably waste a lot of valuable time learning the wrong things. Once you've reached an intermediate level of competence with theory, there are many options, the aforementioned Berklee and Macprovideo among them. For a couple of cheap books that could keep you busy for years, Ted Green's Chord Chemistry and Modern Chord Progressions are still as good as anything out there. I'll admit to getting bogged down in my first attempts (hence the advice to take a theory course first). Not a theory only course per se, but the Guitar Chords 101 course at Berklee is a great starting point before diving into these books.
Cover Songs and Techniques of famous players/styles
LickLibrary - this site has hundreds of different videos on a wide range of topics and styles. They are mostly rock/metal oriented, but they cover a variety of styles. A large portion of their offerings are their "how to play" series which covers songs by most of the popular rock bands/guitarists of the last 50 years. Van Halen, Zeppelin, Floyd, etc. are all covered and they go into note by note lessons on their popular songs. Another rabbit hole down which you could disappear forever. They also have a large number of technical and theory related courses that aren't genre or artist specific. You can probably find a free lesson on every song and style they cover, but you'll probably have a hard time finding such a large number of very professionally produced and packaged lesson plans.
Homespun - have to mention this site as you will find more tutorials on folk, bluegrass, and similar styles here than just about anywhere else on the web. This company has been around for a lot longer than the internet, and many of their offerings date back to the 70s and 80s. They also cover a large variety of instruments - guitar, keyboards, fiddle, mandolin, banjo, etc. Another rabbit hole waiting to swallow you.
Vocals
I admit to not having quite as much experience in analyzing the large number of different vocal techniques available. I've tried Per Bristow's instruction and it wasn't quite working for me, although I didn't spend a lot of time with it in fairness. My second attempt has proven to be the one I'm prepared to stick with for the long run. Going on one year ago, I googled my way to Ken Tamplin. Ken is a long time vocalist, guitarist and vocal coach to a long list of singers both in person and through his video series "How to Sing" through the Ken Tamplin Vocal Academy. This is another resource that costs money, and the full program isn't cheap. I think I paid around $300 for the full level 1-3 program which includes hours of videos, written tutorials, and the mainstay of the program vocal drills for male/female singers. I can safely say that Ken Tamplin has had the single greatest impact on me in the shortest period of time in any of the disciplines I've pursued. In one year I've added power, range and tone to my voice that I thought was unreachable. I've still got a long way to go, but even now I think that $300 was cheap considering what I've gained. Never mind the over the hill metal head vibe he exudes (not that it would, ahem, remind you of anyone), you just have to check him and his students out to see the results. He has quite a few free videos on youtube as well.
Bass
Another area in which I'll admit to not having explored all the options out there. For bass I spend a great deal of time just learning things by ear, and I should acknowledge the influence and inspiration I derive from Geddy Lee, Chris Squire, Sting, Jaco Pastorius, Steve Harris, and many other great bassists. I have used Scott's Bass Lessons, which is a fairly comprehensive site with plenty for beginners and intermediates. He has a channel on youtube with a bunch of free material as well.
Drums
Another one that's similar to vocals in that I haven't been doing it as long and I didn't have to look very far before I found a great resource. I pretty quickly found Drumeo and I haven't looked back. They offer a subscription based lesson plan for their site and they also have some really comprehensive instructional packages. I started with Jared Falk's Successful Drumming, which is a great overview of drumming, starting at a very basic level. I eventually switched to Mike Michalkow's Drumming System, which shares some similarities but is more oriented to learning how to fit in a band as a drummer in a variety of styles (rock, blues, funk, reggae, etc.). Drumeo in general, and these two packages are also very deep rabbit holes in which to dive. Continuing the theme, they also have a ton of free stuff on youtube.
Keys
I've mostly learned by sheet music and by ear. I have taken one course (Berklee Keyboard Method) which was a great introductory course. Besides the above, I've learned odd bits from youtube and macprovideo.