This Instructable is a longer version of the article that appears in heavily edited (in a good way) form in Make magazine, Volume 5. While the editors did a great job of distilling ramblings that far exceeded the word limit I was given into a concise and useful article, the limits of space prohibited much of the additional description, background, nuance, and pictures (larger versions of all the images in this Instructable are available in this Flickr set) of my original piece. So, I thought it was worth posting my first draft. What it lacks in polish I hope it makes up for in depth.
Note: Like most thick magazines or paperback books, MAKE is perfect bound: individual leaves (a leaf represents two pages, front and back, on one sheet of paper) are collected and glued directly to the spine, where the front and back cover (a single continuous wrapped sheet) meet. Shorter magazines are often saddle-stitch bound (longer sheets, representing two leaves each, are folded and stapled at their spine), which actually cuts out a number of steps for hand binding. If you've decided to bind a saddle-stitched magazine (or several into a single book), you've saved yourself a lot of trouble and can skip ahead to Step 4 ("Stitch the Signatures").