Recs.
Updated
Microsoft OneNote is a note taking app by Microsoft that also comes with to-do list feature.
SpecsUpdate
Pros
Pro Offers flexible encryption
Unlike most other apps, you can selectively password protect, and fully encrypt, individual documents or entire folders. This is especially important to many people with data stored in the cloud. As of early this year, even the free version supports encryption. Microsoft has also enhanced their internal security methods for storing data on OneDrive (where OneNote performs sync), which makes it more secure than most of their competitors (including Evernote).
Pro Easy to transfer notes to OneNote
OneNote offers quick and easy transfer software which allows the user to import from other services.
Pro OCR features for iPad
OneNote for iPad has support for handwriting with a stylus as well as optical character recognition. OCR enables you to search for and extract text from images or handwriting in your notes. This is particularly helpful when capturing an image of a whiteboard or other text from your environment.
Cons
Con Not free/libre
This application is proprietary, and thus cannot be modified or freely distributed.
Con Limited storage
Every user receives 5GB of cloud storage through OneDrive (it used to be 15GB). This can be limiting, especially if OneDrive is being used to store other files as well. Add a few videos into the mix inside of a note and it will be easy to max out this storage quickly. More storage of course can be purchased, but may be too costly for some.
Con Platform dependent
OneNote for Mac for example is very different from OneNote for Windows. Because Microsoft has a vested interest in making sure the Windows version is superior, the Mac version tends to lag behind in terms of functionality. Tutorials and other forms of documentation available online generally apply only to the Windows version, which implies non-Windows versions are undocumented.
Even worse, because the documentation rarely, if ever, indicates it only applies to Windows, it's easy to waste hours trying to make non-existent features work. As such, the documentation is "negative documentation" (i.e. worse than no documentation at all).
Con No good way to print (paper, PDF, or any other neutral file format)
OneNote pages are semi-infinite (like excel) and great for taking notes in the application, however there is no Page Break view (unlike excel), or any other good way to export your note to someone not using OneNote (ie. teachers, colleagues, supervisors, etc). Neutral file formats exist for a very good reason, and OneNote does not have a professional way to do this (because it comes out as an uncontrollable garbled mess).
Con No notifications
The OneNote app can be used for a to-do list, but it features no notifications or due dates.
Con No way to generate a list of actions or flagged items from the notes
If you are keeping notes from various parts of you day in OneNote and keep writing list of things that you need to do - e.g., list of grocery items, homework assignments, books or movies to check out and errands to run, these are scattered across different pages. Even if these are tagged with different tags there is no way to filter all the actions (in one notebook section or entire notebook or across notebooks) that have a certain tag.
Recommendations
Comments
Flagged Pros + Cons
Pro It is easy to transfer notes to OneNote
OneNote offers quick and easy transfer software in order to import from other services.
Con All files must be stored in the cloud
OneNote does not offer support for local storage.