* ShoutOut: ''Anime/MartianSuccessorNadesico'', ''VisualNovel/{{Kanon}}'', ''Manga/GreatTeacherOnizuka'', ''Anime/SerialExperimentsLain'', ''Anime/HaibaneRenmei'', ''VideoGame/BaldursGate'' (see Boo and Largo), ''VideoGame/NeverwinterNights'', ''VideoGame/{{Quake}}'', ''Webcomic/PennyArcade'', ''LightNovel/HaruhiSuzumiya'', ''Manga/PitaTen'', ''Anime/DiGiCharat'' and many others.
* "[[http://megatokyo.com/strip/9 Does anyone here]] [[Film/{{Airplane}} speak 1337?]]"
* ''Manga/CardcaptorSakura''. [[{{Lampshading}} Kero seems to realize this in one of]] [[http://megatokyo.com/strip/194 the earlier ones]]
* [[http://megatokyo.com/strip/1249 The book Miho's reading,]] ''Moonheart'', is by Canadian fantasy writer Creator/CharlesDeLint.
* Maybe more of an in-joke than a proper ShoutOut, but reference is made to a [[VisualNovel/{{Kanon}} Shiori walkthrough]] when Yuki goes looking for Miho.
* The Sonoda family, particularly Yuki and her mom, have several ''Manga/KaitouSaintTail'' shout outs. Meimi has the same name as the main character, Yuki's ponytail looks St. Tail's except black, and the whole ImpossibleThief kleptomaniac-thing could be a shout out to St. Tail being a {{Kaitou}} as well as a MagicalGirl.
* The butler in [[http://megatokyo.com/strip/1032 this comic]] seems to have a striking resemblance to Walter from {{Hellsing}}.
* [[http://megatokyo.com/strip/1259 This comic]] has a shout out to the "rice bowl" scene in ''Manga/KOn''
* Largo's [[http://megatokyo.com/strip/771 main]] [[http://megatokyo.com/strip/772 is]] [[VideoGame/GuiltyGear Johnny]], [[EnjoKosai Junko's]] [[VideoGame/GuiltyGear main is Jam Kuradoberi]]
* The first page of [[http://megatokyo.com/strip/1270 Chapter 11]] has Piro in jail next to [[Website/FourChan Pedobear]], whom he apparently beat the everloving crap out of.
* Also, in [[http://megatokyo.com/strip/523 this comic]] Piro is wearing a shirt that's a little too similar to the titular character of ''ComicBook/JohnnyTheHomicidalManiac'' to be coincidence.
*** Coincidence? Piro ''IS'' Johnny in that omake. [[http://megatokyo.com/strip/524 This page]], which just so happens to come right after the one mentioned above, should look very, ''very'' familiar to anyone who's read [[ComicBook/JohnnyTheHomicidalManiac JTHM]].
* The title of 1099 is [[Literature/SnowCrash Piro Protagonist]].
* Yuki proved the Series/{{Mythbusters}} [[http://megatokyo.com/strip/1302 wrong]]. [[note]]Sure, it's a saying, but he does point it out in the bottom corner.[[/note]]
* [[http://megatokyo.com/strip/641 This]] looks a lot like [[Anime/KujibikiUnbalance Ritsuko's helm]].
* Its not uncommon for people to enter Piro and Largo's room from downstairs through the loose floor panel that has a teddy bear sitting on it the exact same way Keitaro would often enter Naru's room in ''Manga/LoveHina''.
* You can see an upside-down CompanionCube [[http://megatokyo.com/strip/1307 on the shelf behind Piro.]]
* [[http://megatokyo.com/strip/1310 Is Piro going to ask random people to become]] [[Anime/PuellaMagiMadokaMagica magical girls?]]
** This is taken further when [[MagicalGirl Yuki]] sees what looks like [[Anime/PuellaMagiMadokaMagica Kyubey's head]] [[http://megatokyo.com/strip/1312 bouncing down the staircase towards her]]. [[CrowningMomentOfFunny Her reaction is understandably one of horror]].
* Kimiko is dressed as Anime/ALittleSnowFairySugar in [[Anime/ALittleSnowFairySugar this strip]].
* Erika is wearing [[Anime/{{Mahoromatic}} Mahoro]]'s gun in [[http://megatokyo.com/strip/310 these]] [[http://megatokyo.com/strip/329 three]] [[http://megatokyo.com/strip/332 strips]].
* Erika and Boo have a debate over Puella Magi in [[http://megatokyo.com/strip/1337 the 1337 strip]]
* [[http://megatokyo.com/index.php?strip_id=1346&q=meta%3A%22Story%22 Kobayashi tells Yuki]] to [[LordOfTheRings "Fly, you...]] [[BilingualBonus baka]]" in the last panel.