Plain Text:
Pros > Simplest, works everywhere/on everything, scales well (append forever!)
Cons > Least automated, no images, no math, no code, hyperlinks depend on editor, no embedded files
WYSIWYG Doc Editor (Word, Writer, etc):
Pros > As easy as plain text, can do images/math/hyperlinks/embedded files, somewhat portable
Cons > Bad at code, not many automated features, unwieldy once file gets large
Markup language tool (Org-Mode, Wikis, etc):
Pros > Powerful, portable, good at code/links, scales well, highly configurable, highly scaleable
Cons > Have to learn the markup language, mostly bad at math, high up-front costs (e.g. needing to set up a server or learn alien keyboard shortcuts), non-wysiwyg feels less like a "quick note" and more like a professional document, image/doc embedding can be hit or miss
Note-taking app (Onenote, Evernote, etc):
Pros > Automates lots of note-taking tasks (e.g. time stamping/tagging), can do images/math*/hyperlinks/embedded files, scales... fairly well
Cons > Least portable (dependent on app-specific sync features which may change), less simple (best use of notebook features are non-obvious), still bad at code
Electronic lab notebooks (ELNs) (labfolder, benchling, etc):
Pros > Good for organizing/presenting data, embedding files, scale very well, have collaboration features
Cons > Very not-simple (most require either require server config, or you don't own your data), most are somehow still bad at math/code, frequently expensive and not portable
Task Managers / To-do lists (Trello, Asana, etc):
Pros > Very intuitive to use, can sort of embed documents/images, have collab features
Cons > Not good for longer-form notes, bad at math, not meant for note-taking, you mostly don't own your data
Others:
Jupyter/Mathematica can do WYSIWYG text, code, math, data, and images all in one document. However, Mathematica is expensive, and Jupyter is non-trivial to get up and running. These tools are primarily geared towards creating a polished document, and are less good at documenting the evolution of ideas inherent in note-taking.
Personal Diary/Journal software is mostly underwhelming, most of these seem like cut-down note-taking apps sold to the non-tech-savvy