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").
Step 1: Strip the Existing Cover
Use a utility knife and a heavy ruler (a carpenter's square is ideal) to cut about 1/8" from the spine (or as far in as it takes to clear the thickness of the glue).
Not counting the two pages of advertising on a single leaf, which you'll probably feel comfortable excluding from the book (sorry, ofoto), you now have 192 loose pages (96 leaves).
It's not a coincidence that this number divides evenly into six groups of 32 pages each (not counting the ad, which was likely printed separately from the rest of the pages and added to the process just before the pages were glued). Because of the way books and magazines are produced (many pages are printed on large sheets, which are then folded and cut as a group), it's more cost efficient to keep the page count to a number that is divisible by a standard number of pages for a pass on the printer. Even if the magazine ends up being perfect bound, the publisher doesn't want to waste any pages for a pass the printer's already making any more than they want it to make an additional pass for an extra page.
When each group of pages leaves the press, it's then folded and cut to form a signature: a collection of pages that looks just like a saddle-stitched magazine and acts as a basic building block for a longer book.