The fanfic Azuvengers gives the Azumanga Daioh girls the powers of different Marvel Comics characters - Sakaki is the Sentry, Yomi is the Incredible Hulk, and so forth. Osaka learns magic, gets a flying umbrella, and communicates clairaudibly with a man named Steve. She's Dr. Strange.
Metal Gear fanfic The Joy of Battle: Historical Espionage Action is full of stealth puns, especially in the chapter titles. The second chapter is called "Schadenfreude" which includes the word "joy" (freude in German), also the main character's name. The most bizarre is probably the chapter "Stained Glass" in which there is a moment near the end where a grassy lawn is stained with blood. Stained grass... incredibly lame and probably entirely on purpose.
ThisPokémon fan comic has a Stealth Pun that doubles as a Shout-Out. The pun in question is the species of the Pokemon, Quagsire... which is based off the word Quagmire, which also happens to be the name of a legendarily perverted character from Family Guy.
Before leaving the courtroom, the half-eagle Gilda Griffon flips out, going in a Mood Whiplashing fit of rage, complete with extending her middle talon at Phoenix. Flipping the Bird anyone?
Like the show, the author of Equestria: A History Revealed seems to love any kind of pun, ranging from horse related puns, to any kind of pun that can be mustered. If there's a word that can be substituted for a horse pun, you can bet it'll be used. Not even the bibliography is exempt from this. The sources are chockfilled with bad puns too.
"Ravished by civil wars up the ass (no pun intended, the deciding battle was fought on Donkey Doodle Peak), and saddled with the responsibility of repairing the broken nation, the new griffon government desperately needed supplies and help."
In the Homestuck fan adventure Alabaster The Doomed Session, there are a lot of hidden jokes about various stories, such as "Beros-Keros" for a giant doghouse, in reference to Keros-Beros from Card Captor Sakura. However, most of the jokes are Homestuck-focused. The [LE] arc is nothing but a giant pileup of Homestuck stealth puns, down to its title.
In the Medaka Box fanfic World As Myth, Hinokage mentions that Maguro thought Unknown Hero deserved analysis. Analysis is also the name of Maguro's own Abnormality.