GoodNotes - GoodNotes lets you take notes and annotate PDF documents.
Xmind - Xmind is a brainstorming and mind mapping application.
OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
Notepad by Braden Farmer - Notepad is an app by Braden Farmer that offers features that let you write and save plain as well as rich text notes by using HTML or Markdown.
Coggle - Coggle is a simple, beautiful, powerful way of structuring information.