How I've wound up taking my notes
If you're going to take and keep notes, you need some way to actually do this. I'm not going to claim that my system is at all universal; it's simply what has worked so far for me. I'm a brute force Unix kind of person, so my system is built on simple basic Unix things.
My basic form of note taking is plain ASCII in Unix files. I don't version control them (although maybe I should), but instead I treat them as logs where I only append new information to the end rather than rewriting existing sections (although sometimes I'll add an update note directly in place next to some information I later found out was incorrect). The honest reason why I take this append only approach is that it's easier to write, but I can justify with it as creating a useful record of my thinking at the time.
(The exception to this is when I'm writing and testing things like build instructions or migration checklists. If my output is going to be documentation for other people, it obviously has to get rewritten in place so the end result is coherent.)
Some but not all of the time I will date new additions to files (in simple '2015-12-30' form). This helps me keep track of when I did something and also how long it's been since I worked on something. Although I often used to just summarize the commands I was using and the output I was getting, I have tried lately to literally copy and paste both commands and output in. I've found that this is handy for being lazy when repeating things; I can just copy-and-paste commands from the file into a terminal window.
I use file names that make sense to me, although not necessarily to
anyone else. Typical file names are things like
cs8-oldmail-weirdness. Often I'll put a summary of the project
or issue at the top of a file, so that if (or when) I look at it much
later I can remember what it was about. For lab notebook stuff I tend to put the date of the initial incident
in the filename, but I'm kind of inconsistent in this.
I've found it useful to segregate my notes files into more or less three directories. One is for (active) projects, one is for general notes on various things, and one is for lab notebook stuff done during (semi-)crisis situations. In all of those directories I have subdirectories for files that are complete, or over, or now obsolete for various reasons. All of these old files remain valuable so I keep them, but I try to keep the top level directories only having current things (especially for the projects directory). I sometimes rename files when I move them into subdirectories because I realize that my initial file name is not a good one for future reference (often it turns out to be too generic).
I don't currently keep any of these files under version control. Maybe I should, but at the moment it feels like overkill given that I never want to delete things and I don't really have a situation where I want 'revert to (or look at) previous version of a file'. Many things are implicitly versioned just by me having multiple files and starting new ones for new situations, even if I copy things from an older file.
(For example, the test plan for upgrading our mail server from Ubuntu 10.04 to 12.04 is in a different file than the test plan for upgrading it from 12.04 to 14.04, even though I created the latter from the former.)
As to where these files all live: their master location is in my home directory on our fileservers. On the rare occasion that I need to refer to or work on one of them when our fileservers or our Linux servers are going to be down, I rsync the relevant file to my office workstation and work on it there, then rsync it back afterwards. These are fortunately not the sort of notes that I'd be looking at if our entire infrastructure fell down. Putting them in my fileserver home directory means that they're automatically available on all of our Unix servers and they get backed up via our backup system and so on.
As for the editor I use, well,
vi is my sysadmin editor. But the choice of editor doesn't really
matter here (and sometimes I use others).
PS: I'm lucky enough that none of my notes files need to be kept so secret that they need to be encrypted. I don't know what I'd do if I needed that for some of my notes, and given that encryption is generally a pain I hope that I never have to find out.