Here’s how I organise my stuff.
I keep very, very little on my laptop. That’s partially because I want ready access to my designs, and partially an unreliable laptop. Really just PDFs there.
I keep a wiki at wikidot for most of my exploratory ideas, first drafts, and noodlings with system. I started using the wiki because I wanted to organise my ideas. Turns out that organising your ideas is a very bad idea. Why? Because I found that this system might go better with that situation, or this setting needs a mechanic from another game entirely. So I try to keep the ideas as small jigsaw pieces, and link them together if the whole looks promising.
I use Google Docs for editing work, and for some more finished texts that I want other folk to take a look at.
Google Reader is for inspirational art, text, quotes, or bits of other people’s designs.
Tasks is for… tasks.
And if I’m in a dull job with no net access, there’s always a tiny, 6-point font Notepad window smeared across the bottom of my desktop.