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.
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.