I'm specifying console games because otherwise this is just going to be a Blizzard and flight sim love-in.
We all know that manuals are basically dead these days, but does anyone remember manuals that really impressed them? The two favorites that I can remember are the manuals for Shadow of the Colossus and We <3 Katamari. Shadow's manual is laid out horizontally with one page being reserved for each action in the game. It was both a unique and simplistic layout, which really accented the style of the game itself.
We <3 Katamari was also done in the style of the game. Many of the control descriptions were laid out like a comic book, and every page had unique illustrations. Sometimes they'd even take a break from game information for a page or two just to have a drawing of the characters doing something.