One of the other functions notebooks occasionally fill is as evidence in patent hearings. If that's a consideration, pencils are a no-no because things can be changed. Yeah, I'm at the "get off my lawn" age these days, but best practice for patent cases is still bound notebooks, numbered pages, ink. If you screwed something up three days ago, you don't erase and fix, you redraw on a new page with the current date and refer back as "corrects version of this on pg 23." For personal use, that's overkill.
I ended up with a piece of home-grown Perl/Tk code that lets me do notes from the keyboard, simple drawings with the mouse, paste in pictures and files, etc. Uses what appears to be the old xterm "fixed" font because at one point I planned to have a version that multiple people could view across the network and I wanted pixel-level sameness across locations. Multiple colors because as you say, sometimes that helps with clarity (and if I go back to add another observation on an existing page, I use a contrasting color for the text). Every line of text or drawn element gets timestamped and recorded -- that's for my own use, and is certainly not good enough to stand up in court. No limit to how far a page can grow down or to the right, which creates its own set of problems. I'm probably the only person in the world that would find it useful, but it does get some of the job done.