I have a small bound notebook that I keep my log in. It's a running journal type format, meaning it's kept in date order. Each time I have something to record, I add the date and make the log entry. It usually includes notes when I'm planning a recipe, calibrating boil-off volumes, tasting beers, observing fermentations, etc. There's not much of a fixed format to it. Particularly during brew days, I tend to record temperatures, volumes, etc, mixed in with comments---usually about things that went wrong or may be unusual, in case they're helpful for debugging later. I also always enter a full copy of my as-brewed recipe for each beer (I develop the recipes on the computer, but I want a hard copy for posterity, and it's already helped me figure out why one beer came out too dark since I dutifully recorded using twice the planned chocolate malt).
The journal-style organization is nice because, in addition to storing the details about beer production, it serves as a reminder of how things played out in time. I can browse back and see my techniques evolving, remember why I started doing particular things, and sometimes just remember which beers were being produced or consumed when. I can see that organizing by recipe would have some benefits, but for my purposes, I like the historical emphasis that this format provides.