I found CraftMemo (Craftmemo.com) through this thread, and I just have to say that it is the greatest thing ever. Apart from maybe the running total of what all your stuff is worth. That's just scary.
I'm going to work hard this month to get all my stuff in to CraftMemo.
Apart from that, I print of internet patterns I want to make, and put them in a binder organized by type of thing (housewares, mittens/gloves, scarves/shawls, etc).
For Summer of Stash, I made an Excel spreadsheet that listed all my yarn, and then had it calculate how many kilometres of yarn I had in total. 8km. eek.
While I had everything out and was digging through it to make that spreadsheet, I took photos of all the yarn, with the pattern I wanted to use it for. If I didn't have a pattern I just took a pic of the yarn.
But now, it's all going in to Craft Memo.