I have used all manner of organisation tools but at the moment the one that is really working for me (and indeed which is telling me I need to write this post) is Thinking Rock. A Java application based on the NetBeans RCP that implements the GTD process.
The basic elements of the application are okay, focussing on quick capture of thoughts and providing enough tools to correctly categorise them. However it is in reviewing and working on your actions that the application really shines. A single screen allows you to review and organise both projects and tasks. The filters for managing tasks are excellent and really make it possible to work with hundreds of thoughts and ideas at the same time. Better yet as a Java Swing programme you get exactly the same functionality and features on OSX and Windows allowing me to use it on all the various computers I own or use at work. A fully-fledged version 2.0 is promised soon but the development version I have been using has been completely stable and fully featured for my use.
I thoroughly recommend it to anyone else with a cross-platform need.