I though It'd be a good idea to share what tools we are using in getting organized.
to write prose, and as a journal. I take notes here about things that I think when reading papers; chuncks of text from the paper, my comments, graphs, etc. Only part of them end up in an actual paper. Best outliner ever.
for project management because of time handling. I'm trying to implement closed lists here. This is mostly a planning tool: I want to see how many hours (estimated) I need to complete each project. Each task should be doable, with action verbs (see 43folders post on verbs for todo lists). No goals here. The total number of hours left is displayed at the top of the tree, and I use that to see if I'm making progress. That is why it is important that the stuff in TodoList is a closed list: otherwise, I know I'll add more tasks, and the counter will go up.
All tasks in this list should have a time assigned.
This is a small notepad-like application written in ahk. It comes bundled with activaid.
Small tasks that come to mind, INBOX: use the "write it and forget it till tomorrow": E.g.of tasks, browse for a tablet pc, post DC. I batch those and do them when doing 'recreational' surfing. This, I do in a completely separated context, (e.g., outside my place: I'm working from home now), to make sure that there is a clear enviromental separation. QuickNote is like scratch paper, nothing stays there permanently. Quicknote is also good for next actions (it is done by date). Ideally, I should follow a 'do it tomorrow' approach in quickNote.
mindMaps/concept maps http://vue.uit.tufts.edu
Currently torn between oneNote and mind mapping. I started using mindJet MindManager, but I found that (for concept maps) VUE is better. It's one of the few java applications that I like and use.
Agenda at once, but it's losing importance
EDIT: Tracking time with time keeper http://www.crypto-central.com/html/timekeeper.html