Wow... what a question!.. Got a year or two? You're right about Moodle being open ended, so much so that it is essentially impossible to know everything about it, which is what you are asking. The biggest question is where do I start?
Bit of background, I started my involvement with Moodle ages ago with a friend loading it onto a server of an NGO late at night unknown to anyone as an experiment in setting up an application and getting it to work. What we found was interesting, so we experimented a little. We saw some things that could be really useful and other things that were not. The idea of Moodle was sprung onto the organization, unexpectedly and they allowed us to run with it. I became the Admin and have been so ever since, as well as being the Admin for a couple of school Moodles I have worked at, still am for one. That was for me the best way of learning how to use Moodle, by finding out what was needed, what did we not need, what is not useful in this setting, and most importantly, how to assess what is useful here, but not there. Different organizations have different requirements, so find out what is common between them, what is not.
For example, Messaging is useful for my NGO but proven a tool for harassment and online bullying at more than one school. The progress bar has been handy for the NGO but the schools have been very slow to adopt it. One school I have been at, uses its Moodle, essentially, as a repository of pre-existing worksheets, videos, and other downloadable resources. Seems it was promoted that way initially, and nothing has changed, made me very unpopular when I suggested that Moodle could be used for a lot more than that. Which reveals the largest hurdle to using Moodle, generating resources, activities, quizzes etc, takes time, unless you have a dedicated team, which can be expensive. All you can do is encourage people to keep plugging away at it.
New tools and ideas are developed all the time so it can be difficult to keep up with the changes. Improvements to older plugins are also ongoing, so when you update, check your plugins, make sure there are new versions available; if not, then it is likely a warning sign the plugin is losing traction, look for something else.
Video can still be a bit of an issue in Moodle, so the POODll group of plugins are very handy, and being updated regularly. These also include a number of other AV tools that can be useful.
My personal wish list has always included a marrying of Moodle and Wikimedia, and with LTI capabilities this is a lot closer than it was, but full integration would, for me, be a much better option. (Not likely to happen anytime soon though.) WordPress can also be accessed via LTI, and the integration between Moodle and Mahara, in Mahoodle, has long been established. Outside of that, I wouldn't recommend anything as a "supplementary" to Moodle, but likely your organization is already using tools that could be considered as supplements.
I could go on and on, but the bottom line is do whatever you think will work for your need. Don't be afraid of trying new things, but don't implement them because they are new, implement them because they meet and are useful to your need. Do whatever works and just ignore anyone who talks about "best practice", they likely don't know what they are talking about. "Best practice" is what gets the best results and outcomes for your clientele, not what some clown on the other side of the world, who has no idea of your particular circumstances are, says "this is best practice."
Good luck, and have a good adventure with Moodle, I certainly have.
