I really like iThoughtsHD for mind mapping. It's very useful when planning any kind of writing, or a presentation, or a paper, or even a thesis chapter. I wouldn't be without it now. And I never used mind mapping in the past.
Another very useful app is Goodreader, which is a superb PDF viewer, and lets you annotate PDFs on the iPad - particularly if you have a (can be bought cheaply) squidgy stylus to scribble on the screen. With this app I find it much easier to read PDFs on my iPad than on a desktop or laptop computer.
And my final big tip is WriteRoom, which is a distraction free writing environment. Unlike Word it doesn't have lots of fancy formatting things, and is all about getting the words i.e. content down, not fiddling with the styles. And that is very good for productivity purposes. You can customise the display. I like mine green text on a black background - child of the 80s ha!
I blogged about the iPad as a productivity tool on my academic blog at
https://vivsacademicblog.wordpress.com/2012/10/16/the-ipad-as-a-productivity-tool-and-some-recommended-apps/
and
https://vivsacademicblog.wordpress.com/2012/11/06/more-thoughts-on-the-ipad-as-a-productivity-tool/
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