It’s a little dated but The CTDP Linux User’s Guide is an excellent linux reference, covering everything from Bash to X to user management, to heaps of stuff.
I like the layout because it reminds me of the reference guides we had at Melbourne Uni. Simple and to the point.
Another great reference, which is also useful for Windows and Oracle also is the ss64.com site. It is just a collection of manuals and other reference documentation useful to have around when you simply need to get to manuals.