Outlines

I think that those who are aware of mind maps and outlines (I explore the differences in some detail in The Productivity Habits) tend to use one or the other. I like to use both together, but for different and very specific purposes. Mind maps, being visually clear, are great for the speedy capture and analysis of information. For complex projects, like writing a long paper or a book, a plan for a multi-phase project, or deconstructing / synthesizing an argument, a tool which offers more detailed control of structure is essential. 

While mind maps allow you to represent a cascade of information on a two dimensional plane, an outline represents the same cascade in the manner of an indented list which you would read top-down. Because of this, outlines sit somewhere halfway between a mind map and a block of text.

This is useful because it makes it easy to add lots of information to a node on an outline. A node on a mind map shouldn't really contain more than a short sentence, but an outline makes it easy to expand this, even up to a full paragraph. Even so, a branches can be collapsed, moved around, and the whole document restructured just like a mind map, allowing you to fine-tune the structure.

OmniOutliner

My outlining weapon of choice is OmniOutliner. From the same developer as OmniFocus, my task manager of choice, I've benefited from the same level of reliability and customer service that would be expected from a relatively expensive suite of software. It's currently available for Mac and iPad, and will shortly be shipping for iPhone as well. I find the software to be clean, logically-laid out, and capable of producing attractive results which is important for a form of information which lends itself to presenting complex concepts and plans. 

I do find synchronization to be a challenge as OmniOutliner doesn't yet support any of the most common syncing services. However, I rarely use outlines to capture information so ubiquity is less important than outlines, and according to Omni Group's 2015 plans this will not be a constraint for much longer.