I tried to use something like Confluence server, but it kept causing issues with JIRA and Bitbucket servers. I really like the ability to "connect" wiki entries to issues and repos, but really needed to find a more accessible way of organizing personal projects, educational notes, etc.
So, I started using OneNote - and it's perfect for categorizing 'bookshelves' of information, and even securing pages. I felt that this was the best option since nothing seems to be hindered by a paywall (like Evernote, for example) - plus OneDrive (5gb) and pretty much a free suite of Office comes with it, too. Mostly everyone also has a Skype account, which is actually a Microsoft account now, so there are no other accounts required either. Just login to OneNote.com with the one you use for Skype, and there you go.
I keep an entire reference guide to Bash CLI that I've written myself, use Pocket as a bookmarking system for articles I don't want to have flood my toolbar of favorites - and, now reference them in OneNote.
And this is coming from a guy that used Notepad++ for everything, a decade ago. :P
Creative Technologist & Sr. Front-End Developer