Getting organised for a bigger research project

People who know me know that I like ideas, creativity and the process.
I want to throw myself into finding out. Problem is, it's like
decorating: I want to get the effect without sanding the wall. What
I'm thinking about here is doing the groundwork that will support my
research.

Here's a few questions:

- what's the best way the manage bibliographic information?
- how can I keep a track of my thinking and revisions to that thinking
as I go on?
- how do I relate ideas (and later on capture, present and analyse) findings?

OK, to most of us not a hot topic for a blog post: but as a note to
self, it's important, right?

Here's a few things I'm doing to 'tool up' for my PhD research. I will
add to it, but it's a start:

- I'm using del.ici.ous social bookmarks to capture and share up
information on the net.
- I'm checking out bibliographic software like endnote (thanks, Suzie
in the library service).
- I am checking out the bookshelf tool in Google Books
- I'm writing this blog (obviously)

BUT I've yet to find a good a good way of taking (and more importantly
managing) notes - on books, ideas, sketches. I know I could (gasp) use
real paper note books, but they are less good for managing, re
ordering and playing with connections between ideas. Perhaps Google
notes would work, but it's a product they've stopped supporting, so
I'm not keen to invest my eggs in that basket. What about One note? :
evil Microsoft software based solution.

I need a web based portfolio that lets me throw in sketches, photos,
traditional notes, audio recordings and more.

Any ideas?