I learned to keep detailed, highly organized notes while working as a field biologist as a young man. In those days, if you were lucky enough to be museum trained, you used "The Grinnell System", which was a binder-based system that specified everything from the kind of ink to use (high carbon, black india ink), the paper (acid free high cotton bond), and layout elements, such as the locations of margin lines, dates, and page numbers. Tabbed sections were used to organize notes by activity. We used 8 1/2 inch binders because the smaller size was easier to use in the field. I spent many a long rainy night, usually in a tent or the front seat of a truck, completing my notes of the day's observations. My notes are now deposited in a museum, where they can be accessed by researchers working in the regions I used to haunt.
These days, as a statistician, I still take copious notes. But the ink and binders are gone (and so are the ticks and mosquitoes!). Organization is key: I need to record the entire data analysis process, from data formatting and cleaning, to graphical analysis, coding for models and processing scripts, and finally construction of figures suitable for publication. I looked long and hard for a digital note taking system before finally settling on NoteTaker by Aquaminds. I think it's binder-like system appealed to me, after so many years using binders in the field. I've been using NoteTaker now for at least 7 years.
NoteTaker is not completely free-form like some systems: note books mimic lab books in style and format, with digital pages in a digital binder. You add discrete entries, which are organized consecutively like an outline (entries can be moved around in the hierarchy). There is a table of contents for each book, and tabs are used to organize books into sections, much as a physical binder. Content can include everything from text to jpegs to sound files and video and everything can be time-stamped. Auto-indexing is a useful feature, though of course there is a built-in search utility, too. Notebooks can be ported to PDF, and there is a free reader for sharing notebooks with people who haven't purchased NoteTaker.
I've used NoteTaker for many academic and professional projects over the years. I've grown to rely on it as my main method now for keeping track of projects. It's not the Grinnell System, but for people trained on a binders, it feels like a natural replacement.