How do you organize your GM threads?
It depends on the game and time and effort I am putting in, but I definitely feel the point about doing lots of organising under the guise of productivity!
I try and keep everything in one Word doc on my laptop with headers. I'll have a header for every character containing their background, what I think their motivations are (either because the player has told me or it is coming out in play), what story hooks are emerging, their relationships to other characters. I also do this for NPC's and spend a lot of time hyperlinking and separating 'in-game' knowledge and 'in my head ideas' or 'secret to players'.
I have a story so far with all the story points and a short list of 'the next three big things' that I want to happen / could happen and a short list of 'things that may happen / interesting points'. I'll have a timeline - what's happened, what's going to happen next to push a story on and what's happening outside of the player's attention.
I also do a big visual relationship, story hook and event map to try and capture a 'whole story picture' - I'm loose with my definition here, but when I have this map I can see where there are gaps, where people are more involved in the story than others, what I need to pull others in and any hooks that emerge from seeing a bigger picture