1. By using Microsoft OneNote, which is free for Windows, OS X, Windows Phone, iOS, Android, and Web @ Outlook.com
2. You don't, you create Notebooks in OneNote.
3. See #2. You then Create Section Groups, Sections, Pages, etc. in those Notebooks for your Notes.
To the person above regarding File Limitations. The only File Limitation worth considering with Flickr is the Video Limit. 3 Minutes @ 1080p resolution. Flickr is, at heart, a Photography services, not a YouTube or DailyMotion replacement ;-)