Someone mentioned project management, which got me to thinking about how I organize projects.
1. I start with a mind-mapper, to basically outline the project. I like Xmind (
http://www.xmind.net/), although there are a number of other Open Source options for this. Think of it as an electronic whiteboard where you can capture random ideas about a project, it's purpose, the processes required to complete the project, breaking the project down into tasks, etc.
2. From here, we go to a project planner, for allocating resources/assigning tasks, establishing a timeline, etc. I prefer the Gnome Planner (
https://live.gnome.org/Planner).
3. Many of my projects require some sort of literature search. For keeping track of key references, there are applications like Mendeley (
http://www.mendeley.com/features/) or Zotero (
http://www.zotero.org/). Key here is the ability to annotate/highlight/write notes while reviewing the documents.
4. For keeping track of my own thoughts, project progress, etc., I like Zim Desktop (
http://zim-wiki.org/).
