In episode 11, after Yuuji and co. declare war on Class D, Akihisa is seen crawling around under a mandarin box towards a couple of Class D kids, with the male one lampshading the move by rhetorically asking out loud, "Snake?" Upon being discovered when the box is lifted, Akihisa quietly imitates the alarm signal sound effect before exiting.
Also a Metal Gear Shout Out with Iron Man coming out of a box, twice including one where he sneaks up on his target in the box. Also might be a reference that the "vent duct maze is part of the security".
Furthermore, in episode 7 when Hideyoshi brings out the walkie talkie to call Akihara, the Metal Gear Solid 4 codec menu pops up on frequency 141.14, a joke towards Otacon's frequency being 141.12 and a joke about controller ports"
Not only do the summons look like the Dwarves from the Class Of Heroes series, the full title of this is a shout out to the Japanese name of said series (Ken to Mahō to Gakuenmono, "Swords, Sorcery, and Scholars").
Darker than Black II — Hideyoshi's Transformation Sequence style of summoning his Being is a Shout-Out to Suou's power activation sequence. It also parodies transformation sequences in general: his clothes disappear at the beginning and then pop back in exactly as they were before.
In episode 2, Kubo summons his beast from his shadow with the same style of Asura Cryin'.
In Episode 7 we see the same elaborate fake drawer bottom set-up Light used to hide the Death Note. Unfortunately, it seems Shouko watched the same show.
Bonta-kun shows up as a background silhouette at the amusement park.
In Episode 8 we learn, that the school Principal seems to get her equipment from N.E.R.V.... Oh Crap! (Might have to do with the fact that her name is Kaworu...) Also, the Third Impact happens for whatever reason, and the eyecatch is a send-up of Eva's episode title cards. This whole episode was one big Evangelion Shout-Out. The Principal doing the Gendo Pose and Smirk. Yoshii yelling father just before the afore mentioned Thid Impact. There's probably more, too.
Adding onto that, "The avatar is here" and Muttsulini's summon becoming a little cannibalistic like a certain type of mecha are also references to EVA.
Apparently, Kouta has a Geass and Himeji has a SEED Mode. Seemingly, Kouta and Akihisa ALSO have a SEED mode, not just Himeji. At least according to episodes 5 and 6. The "SEED Burst" is seen quite a few times through the series.
Episode 8 also spoofs Impulse vs Freedom showdown from Seed Destiny, with Yoshii's summon as Impulse, and a clone of Mizuki's summon as a combination of Freedom and Strike Freedom.
Akihisa doing the Kamen Rider Black transformation pose to summon at the start of the episode definitely counts.
Himeji's and Minami's Adult avatars take on the appearance of Morrigan and Lilith, respectively.
The communicator Yoshii wears on his right hand is a Power Glove.
Yuuji's and Kouta's rampaging Summoned Beings that Akihisa fights in the vent ducts use moves reminiscent of classic Super Robot anime series and Naruto.
When Himeji offers to help Akihisa study for the make-up exam, in his Imagine Spot she's wearing Mizuho-sensei's clothes. The voice actress even changes her tone to resemble that of Kikuko Inoue's when playing the character.
The entire vent duct sequence is a machine gun of Shout-Out gags. Mario underground level, anyone? Complete with Super Mushroom and green piping.
Hideyoshi is an obvious reference to Toyotomi Hideyoshi. His avatar has the traditional naginata/outfit combination, and he talks like an 80 year old, although this is probably lost on non-Japanese speakers since it's hard to properly convey in translation.
Also, his last name is taken from Hideyoshi's old name, Tokichiro Kinoshita, back from when he was a servant of the Imagawa Clan.
The battles themselves have a Shout Out to Valkyria Chronicles: the cut-ins look exactly like those in VC, down to the animation.
In the Opening, the teacher Tetsujin/Ironman strikes a pose similar to Akuma from Street Fighter after a Shun Goku Satsu; complete with a kanji symbol on his back.