I use the old project binder and engineering notebook method. I have projects that are over a decade old and these software apps tend to not be as flexible or as long lasting. Your newer researchers and engineers tend to want an all software solution so you let them test those apps out at their own peril.
I'm a graduate student who is trying to get organized. A thesis is a relatively complex long-term project that involves a lot of research... so I have a lot of tasks and a lot of information to keep track of.
I've found a bunch of software that do some of what I want, but nothing complete. Ideally, I would like a tool (or set of tools) that will let me:
1. capture information (web clippter, note taking app)
2. organize information (mind map software that will let me include files/webpages)
3. plan tasks using that information (todo list, gantt chart)
4. create content that refers to my content library (reference manager, blogging platforms)
Right now I'm using a collection of tools that look like this:<div>
1. capture: Evernote + Mendeley Bookmarklet for PDFs + InstaPaper for web pages
2. organize: XMind for mind mapping, Mendeley for organizing literature
3. plan: ToodleDo for simple todo lists, Workflowy for complex project plans, Excel for gantt charts
4. create: Word + Mendeley plugin for writing papers, Wordpress & Twitter for publishing to web
That's 10 different pieces of software to do tasks that are all related to the process of gathering, organizing, an citing the same set of resources.
There must be a better way...help!