I finished my PhD about a year ago and found some of these very helpful:

most of these are Windows software:

EndNote for organising bibliographies. (check whether your school offers a free or reduced version for students)

IdeaMason for organising bibliography, composing drafts, and exporting to Word (cheaper than EndNote).

alternatively, Firefox extension Zotero, which also looks like a powerful organising/bilbliography tool.

a simple freeware tool for drafting ideas: KeyNote. Development sadly stopped 2 years ago but I still find it an extremely useful tool. Exports in .rtf format

Also freeware, and also very useful is Text Block Writer. Works like a set of virtual notecards to outline ideas for drafts. You need .Net Framework verson 2.0 for this. Exports to .rtf.

EverNote. Clipping tool.

I now generally use a combination of Text Block Writer, KeyNote, and EverNote. But I'll test-drive IdeaMason once I have some spare time, as it looks fabulous. I'm also still waiting for a beta invite for http://iscrybe.com/main/index.php, which looks like a powerful calendar/clipping tool and works on and offline.

As for books, I found these two particularly useful:

Joan Bolker, "Writing Your Dissertation in 15mins a Day" - mostly geared at PhD students, but useful for MA theses or any other longer writing project too

Eviatar Zerubavel, "The Clockwork Muse". On scheduling / organising your writing time and writing zero drafts

online forum:
PhinisheD. A forum for grad students