I agree with a lot of the answers above but would like to offer some extensions to the ideas of context and anchoring.
I think of my mind in a flow state as being like a Smalltalk image - it's a rich binary world and I want the best way to dump and restore it. Textual lists and having things open on the screen are one way but I also try to engage multiple senses. Sometimes, I scribble quick, rough diagrams on paper and either trace them with fingers or redraw as I'm rebooting. These are not accurate drawings but mental keys to suggest a more detailed structure.
One of my more successful things is an audio recording of my thoughts, particularly about what I was going to do next. This is often faster than typing and you can do it whilst brushing teeth etc or often make last-minute recordings of things you thought of just before you drop off to sleep. I use Evernote for this, recording on my iPhone so it's synched up to all my work computers - that way I don't have to worry about things if I have to dash in to my day job and was working at home.
If I'm cycling to work I can listen to my Evernote mind-dump from the night before, mull it over and be in a good state when I get there. If I'm working at home, I do the same thing whilst I'm walking the dog.