I've tried many different methodologies: flowcharts, post-it notes, to-do lists, PIM, etc. but none have worked very well for me. I'm trying a "new" version of an old method - Mind Mapping. I have read many articles and listened to many podcasts that mention mind mapping software but hadn't tried it until recently.
I decided on mindmeister due to it's user-friendly front end, the collaborative features, and the offline mode using google gears. I'll let you know how it goes. In the mean time please let us know what works for you.
I have used the Franklin Covey planners for a long time and still find it effective for task accomplishments. This is especially true due to my poor memory for commitments. I have to write them down and prioritize them.
Mind mapping is good for basic individual brainstorming and organization. Have not been successful using it in a group setting (have tried it a few times).