I'd like to know what people are using for writing non-fiction. Mainly I'd like to know how people keep track of their research and cross referencing it from their editor.

Here's what I have:

* Many words typed up in One Note

* Highlights and annotations in iBooks, Kindle, and Instapaper (although Instapaper allows export to MD)

* Notes from PDF exported to Markdown using the Highlights app[0]

* Images

* Tons of shit to read in pinboard and other places

Here's the kicker, I travel a lot (every week) so I need most of my tools to work well offline/slow wifi and preferably on an iPad/iPhone.

What do people use for organizing notes and research (literature of all sorts), cross referencing, organization, and first draft?

0: http://highlightsapp.net/