Recs.
Updated
Org-mode is a note taking tool to be used with Emacs. It is geared towards authoring documents, taking note, keeping todo lists and planning projects, all in a simple text format.
Specs
Pros
Pro The ultimate note-taking app for programmers/STEM people
Nothing beats it when it comes to taking notes as a programmer. It supports native code highlighting/evaluation, inline LaTeX symbols, Vim keybinding, intuitive hierarchy and folding, instant LaTeX export… and so, so, so many more. Evernote and Onenote etc. can do absolutely nothing when it comes to these aspects. There is even an article describing an experience switching over from Evernote/OneNote at here.
Pro Built-in agenda
Org-mode has some built-in agenda functionality. You can schedule tasks and assign various degrees of importance to each of them. Org-mode agenda can also be synced with Google Calendar.
Pro Basic spreadsheet functionality
Org-mode has some basic spreadsheet functionality. Other than auto-formatting ASCII tables (a notoriously annoying problem), it also has support for LISP-like syntax to define equations or any other functionality that can be achieved through spreadsheets.
Pro Org-mode documents can be published online as HTML, wiki, markdown, asciidoc documents
Pro Notes in Org-mode can be exported to slide presentations in formats including Powerpoint, Revealjs, Slideous
Cons
Recommendations
Comments
Out of Date Pros + Cons
Con Not really cross-platform
You can try mobileorg (that looks kind of abandoned) but there's no easy, out-of-the-box solution.