For diagrams, I used to use XFig on my linux machine, and create documents with LaTeX. At some point, I used Visio, but found it was not flexible enough, and switched to the drawing tools inside OpenOffice on my MacBook. These days, there are many useful online tools that enable you to work with diagrams, outlines and visualise project management, without having extra applications on your computer.
Gliffy has many features that I used in Visio, and is useful for programmers that use UML (at university I used Rational Rose or XFig to create such diagrams - having an online tool like Gliffy would have made creating these diagrams a lot less stressful and time consuming!) From simple flow charts and room plans to network, interface and UML diagrams, Gliffy is easy to use, and seems to support most of the popular browsers.
There are a number of online tools (and other programs) that allow you to create outlines - useful for document planning, project management, knowledge management and software engineering. Most of these outliner tools allow you to 'fold' or minimise sections, fantastic for those who use a top down approach, starting with the big concepts and then drilling down into detail. Office software such as Microsoft Office, and Open Office have an outline mode, and it is an oft-asked for feature in Google Docs. Mark Wieczorek maintains a comparison of outliners on his blog, and Outliner Software is a forum for those who work with, or are interested in outliners.
Mind maps or macrologues, area specific type of outliner, and are useful to explore concepts both in depth and breadth, again using a top down approach. I found that my thoughts are quite circular, and that many interrelated ideas don't result in a nice, clean mind map (is there any such thing). Mind Meister allows you to create an account using your OpenID, such as your Google account, which I find very useful. Mind Jet, iMindMap, VisualMind, and Free Mind are other popular mind mapping tools.
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