The Dresden Files tabletop RPG rulebooks are... unique. They're presented as a rough draft written by Billy the werewolf and handed over to Harry for perusal and correction. As a result, they're full of marginalia written by Harry (complaining about how Billy describes him, making bad pop culture references, and yelling at him to cut out top-secret White Council information), Bob (technical details about magical beings, plus a bunch of dirty jokes), and Billy himself (responding to the other two), who are differentiated by different typefaces, colors, and sizes of "handwriting." There's sticky notes all over the place, Harry occasionally uses it as scrap paper, the illustrations are taped in, and Billy dropped it in a puddle. And when Harry is being used as an example character and starts griping in the marginalia about how he's starting to hate his "player", the fourth wall is in danger of being tipped over.
The second version, Dresden Files Accelerated, does the same thing in a different way. The book is this time the work of Ivy, with post-it note annotations where she and Kincaid argue about puns and swap one-liners. There's even one where they discuss how odd it is that Harry doesn't wear a hat, which goes so far as to have a sticker of the Evil Hat Publishing logo applied.
Used a lot in Magic: The Gathering. For example, in Time Spiral, the timeshifted cards are printed in the old card frame to show that they are from the past; in Planar Chaos, they are printed in an alternate version of the new frame to show that they are from an alternate universe (i.e., they are color-shifted versions of existing cards); and in Future Sight they are printed in a futuristic frame because they are previews of possible future sets. Also, there are numerous single-card examples in the Unglued and Unhinged joke sets:
"Old Fogey" and "Blast from the Past" are both in the old card face. "Old Fogey" also says "summon" instead of "creature".
"Look at Me, I'm R&D" looks like a playtest card.
"Richard Garfield, PhD" looks like a religious painting.
Stone-cold Basilisk has a frame that appears to be made of stone.
Fraction Jackson's text box, art box, and expansion symbol are cut in half.
Topsy Turvy is printed upside down.
Let's just shorten this list by a lot and say that in Unglued and even moreso in Unhinged, you've got probably between a one-in-four and one-in-three chance of a card having a nonstandard card frame.
Art for most cards is confined to a rectangular box in the middle. Planeswaker cards often have part of their art poking out the top of it, into the area usually reserved for the card name.
Done with the rulebooks for Paranoia. Player documents have security level Red, while gamemaster materials are classified Ultraviolet. Since the players' Troubleshooters start at Red level, they are technically guilty of treason if they read the higher-level rules. The GM is encouraged to terminate the PCs if they try to game the rules, and players are encouraged — in true Paranoia fashion — to know the rules but don't let on that they know them...
Game supplements for Shadowrun are often presented in the form of in-character online documents, to which various deckers have appended their own commentary. Often their remarks contain plot-hooks for Game Masters as well as jokes for readers.
In the original Malkavian Clanbook for Vampire: The Masquerade, various pages throughout the book were altered, using mirrored text and other techniques. One of the most dramatic was a page talking about alternate food sources for some Malkavians. As it reached the end of the page it discussed a particular vampire who fed on words — and then featured a picture of said vampire who appeared to be eating the text off the page, leaving scattered words and a large blank area.
What's even scarier, the Malkavian in question was supposed to eat not only words, but also ideas that these words represent. Cue the paragraph about the Word-Eater's diet not only blurring and falling apart under his hand, but at the same time degrading into gibberish ending with an orphaned line on the other page: "...and other butchers' aprons."