I find that using a pen and paper works best for developing an outline and writing initial paragraphs. It’s worth trying to get away from your normal work space. Go to a coffee shop for an hour or so with just a nice pen and a notepad.

I use FocusWriter for when I'm writing up new ideas - brainwaves that I've just thought of and I'm not sure what to do with (or if they're any good). FocusWriter is a free full screen word processor with no buttons, toolbars or anything other than a white screen (customisable to any colour) and your words. You can get a free copy here: http://gottcode.org/focuswriter/ (Mac / Pc / Linux)

Endnote makes the managing and publishing of your references straightforward. The Library has more information on how to use and where to get a copy of Endnote: http://www.tcd.ie/Library/support/endnote/.