* ShoutOut: ''Manga/MartianSuccessorNadesico'', ''VisualNovel/{{Kanon}}'', ''GreatTeacherOnizuka'', ''SerialExperimentsLain'', ''Anime/HaibaneRenmei'', ''BaldursGate'' (see Boo and Largo), ''NeverwinterNights'', ''{{Quake}}'', ''PennyArcade'', ''SuzumiyaHaruhi'', ''Manga/PitaTen'', ''Anime/DiGiCharat'' and many others.
* "[[http://megatokyo.com/strip/9 Does anyone here]] [[{{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 [[{{Kanon}} Shiori walkthrough]] when Yuki goes looking for Miho.
* The Sonoda family, particularly Yuki and her mom, have several ''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 {{K-On}}.
* Largo's [[http://megatokyo.com/strip/771 main]] [[http://megatokyo.com/strip/772 is]] [[GuiltyGear Johnny]], [[EnjoKosai Junko's]] [[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 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 [[JohnnyTheHomicidalManiac JTHM]].
* The title of 1099 is [[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]]
** This Troper doesn't watch Mythbusters. What is Fred talking about?
** Mythbusters once tested "knocking your socks off" with an impact; they couldn't do it with a non-dismembering force, but they easily managed knocking ''shoes'' off. So despite the annotation, the comic is [[MagicalGirl partially]] realistic.
* [[http://megatokyo.com/strip/641 This]] looks a lot like [[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 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.