Then there's Sakuya's massive cruise ship, daringly named Titanic, which eventually sinks just like its namesake. Hayate even ends up swimming in freezing cold water to save a girl similar to the final moments of Leonardo DiCaprio's character, who is also mentioned several times. Of course, this manga also adds sharks.
When questioning the criminals who blew up the ship, Sakuya scolds them for confessing their plan too easily:
Sakuya: That's not how they do it in Conan, is it?
Later on, the entirety of chapter 108 is one big shout-out to Detective Conan. Conan himself appears several times and the main characters dream they are transported to his world to solve a case. It's even named after Conan creator Aoyama Gosho.
Kaito Kid from the same anime appears in episode 30, and Nagi dresses up in a Gender Flipped version of his outfit, calling herself the Great Detective Nagi. She even goes through the trouble of putting a mustache on Hayate so he looks like Detective Mouri, knocking him out, hiding behind him, and using a voice changer disguised as a bow tie to make everyone think that Hayate has solved the case.
And of course, one can't forget the "evil combat butlers" attempting to defeat Hayate throughout the second season, nearly all of whom were blatant Shout Outs to popular Shōnen series. "Duel Butler" was a dead ringer for Shoubu Kirifuda, "Butler B-Da", who looked like the main character from B-DaMan, "Race Butler", who looked like the main character from Crush Gear Turbo, "Butler Nabeshin", "Puppet Butler", who took over people's minds using his Evil Eye (and was voiced by Jun Fukuyama), and "Cyborg Butler", who looked like a cross between Gai Shishiou and Viral, was voiced by Nobuyuki Hiyama, and used nearly all of GaoGaiGar's Super Robot attacks under Brand X names.
The Cyborg Butler also made a Super Robot Wars Shoutout. After Shion said, permission to use Final Hammer approved, a la GaoGaiGar, the Cyborg Butler shouted Drive, a spirit command/spell in said game.
In episode 18, when most of the group has been eaten by a whale, Taiga is shown holding a combination broom/axe, and thinks that their predicament was was Diana's doing.
Also in episode 18, Hayate goes Super Saiyan when protecting Nagi.
In episode 19, Nagi shows Hayate and Maria a strange video, and then claims that she'll die if she doesn't show it to two other people within a week. Hayate exclaims that it's just like that circular video. The narrator himself almost clarifies, but only gets to "Ri-" before Hayate stops him and the opening starts.
When Hayate was cursed to wear girl clothes, he went by the alias of "Hermionie" to avoid being recognized. Other characters commented that it sounded like a wizard's name.
Nagi claimed to be a superior director to Haruhi... this is clearly why Nagi's popularity fell in some of the later polls. Still gets alot of Shout Out's however.
Nagi also comments to Maria that when releasing anime DVD's, you should put the episodes in the order they were broadcasted, rather than their true chronological order. This is another obvious shout out to Haruhi.
In episode 12 of the anime when Nishizawa confesses to Hayate he claims to "only like 2D girls"...and pictures a band with CensorBox eyes with a bunny girl lead singer and a witch playing bass.
Klaus suggests Nagi form a S*S Brigade when she says she's bored
Episode 23. How does Maria catch the Lord of the Lake? It's classified. Her gestures when saying this make it obvious.
Not only do the thugs look like Zangief and Dhalsim, but Hayate gives Zangief a taste of Shoryuken in case someone somehow failed to notice.
Don't forget the new class register, formatted in the style of some manga or another filled with weird students (such as a ghost) and filled with little notes scrawled in the margins. Oh, and apparently some fellow calls himself a 'Mahou Sensei' just to make sure you get it.
Adding more shout out to that scene: Hayate's class number in the picture is the same one as Kaede's, who, like Hayate, is voiced by Ryoko Shiraishi.
In the new class register, everyone besides Hayate and Nagi is wearing a mask similar to that of Friend.
In episode 33 when Nagi imagines Hayate working at a cosplay cafe, she imagines him dressed up as the eponymous sensei from Sayonara, Zetsubou-Sensei, complete with comedic hanging scene.
CathedralTerra made an appearance in one of the latest episode in season 1
There's a brief arc where Hayate is one of the hostages taken by a robber — wearing a seven-eyed mask based on the symbol of SEELE.
In Chapter 192, Spice and Wolf is combined with Baka to Test to Shoukanjuu to produce "Fool and Test and Spice" — with a wolf-eared girl in a school uniform on the cover. Chiharu is a fan of the heroine's speech pattern, but Nagi thinks the best part is the crossdressing boy.
Chapter 148 has an entire page's shout out to Manga/20thCenturyBoys with the whole class being made to wear Masks similar to that of Friend in order to have their photos taken.
The Lucky Star cast has a cameo as posters at a shrine during a quiz game in Chapter 194.
Speaking of Lucky Star, in episode 23, Kagami◊ is apparently one of Hayate and Nagi's classmates.
When two members of the cast go to Las Vegas, there's a fewpanels showing the four guys from the Gaijin 4koma.
He makes a reference to the same anime again in episode 21, when he uses the Dragon Shiryuu's move.
And again in Episode 31, where Nagi "adopts" a pair of street kids who are basically Phoenix Ikki and Andromeda Shun pulled straight from a childhood flashback. The opening even parodies Saint Seiya's dramatic opening narration style.
Episode 33 of the first season had a massive shout out to Nabeshin of all people, where he was one of the obligatory Battle Butlers, though he himself just wanted to draw Moe.
Episode two of season one. While Hayate is at the docks with the Very Nice People, he imagines what's going to happen to him. Among those Imagine Spots are : The crew of the Black Lagoon showing up and a weird shout out to One Piece.
Pay attention to the statue busts in the mansion. Quite a few are shout outs to various main characters.
The fact that in each of the battles you win by either getting your opponent to give up or knocking off their neckties in itself is a clear Utena reference. Oh, Hinagiku also winds up asking for the power to revolutionize her school, and the narrator also directly references the famous "Absolute Destiny Apocalypse," line from the battle theme of the anime.
In terms of the manga, chapter 334 features Ruka dressed up as Kyubey.
In chapter 342, Nagi goes to a store in Akihabara that one of the doujinshi with a pair of girls on the cover that look a lot like Tenri and Diana and a poster in the background featuring Mami and Kyubey.
Chapter 294 in the manga has a poster with Ayumi as well.
The manga (volume eight, chapter six) has Nagi playing a game and noting "this game is divine." A close examination reveals Divine Retribution on the screen. Her companion seems uncertain about the "doggie" being the hero.
One of the episode in the second season, Nagi played a card game, and uses a card which allows her to continuously attack so long as the card she picked up from the top of her deck is a character card, complete with Doro !CharacterCaado !
One of the chapter has a spirit of a dead priest, entering a penguin costume. Sounds familiar?.
When Hayate is told about Hakuoh's high standard, he is stabbed with a Zankantou
In the panel where Hayate wields six swords at once, his stance is very reminiscent of one of burial priests in Fate/stay night and Tsukihime.
One of the events in the anime has Hayate using Inazuma Kick complete with the narrator stating the name of the move. Now, take a look and check the narrator's seiyuu.note Its Norio Wakamoto who voiced Coach.
In the anime filler RPG Episode, a slime's attack animation starts with it morphing into a creepy Rei Ayanami face.
When Hayate is looking for the legendary persimmon tree in the garden, he mentions how it looks like the background from a Studio Ghibli film (Princess Mononoke to be exact).
In Episode 50, Nagi mimics the Ultraman henshin sequence (with relevant sound effects).
In chapter 119, Nagi squirts Hayate with a water pistol after he says that he went into the hot spring. She is disappointed when he fails to turn into a girl. She had really been looking forward to that.
Back at the video shop, Hayate asks Nagi's fiance (forgot the name) about a DVD lying on the table beside him. "Tengen T-" "Bamboo~~~Bamboo~~~"
In chapter 416, Ruka's thoughts are portrayed in a style evocative of Kaiji, including the distinctive "zawa zawa" and the over-the-top narration.
Due to her love for money, Katsura-sensei gets lured away from Hayate while in the Tiger's Pit and sells her body to an evil spirit for 1 million Yen (which she never receives). While possessed, she has the Majin symbol on her forehead.
The first season makes plenty of MÄR references (usually involving Dorothy in some way, shape or form). And considering that both shows at the time were made by the same companynote SynergySP, whom also get referenced in an episode, this isn't too unexpected.