The end of Episode 203 has Gintoki somehow be able to use Final Getsuga Tensho. Particularly funny after a couple of episodes spoofing the idea of a time-skip showing characters as stronger, improved, etc. Gin's reaction at the end of the episode is something like; "No helping it, I'll just have to go with this" Cue transformation.
There are also a few shout-outs to Yoshihiro Togashi's work. Prince Hata is a walking shout-out to Level E (he's even called "Prince Baka" all the time!) although he looks like Fat Buu, and there's an exchange where Gintoki has cornered a villain that is a hysterical parody of the flashback where Sensui and Itsuki meet (sorry, paraphrased):
Gintoki: Do you have anything to say before you die?
Villain: If you'd let me live for one more day, I'd like to watch my favorite TV show.
An episode title: Laputa'sstill good after seeing it so many times. The episode itself has a small part where Kondo, Okita, and Yamazaki discuss their favorite Ghibli films and their different aspects.
Episode 30 is pretty heavy on the crime-solving/detective references, so there's plenty of Detective Conan references. Like the eponymous detective making a quick appearance, only with a topknot/chonmage. Gintoki even grabs a sleeping Mouri look-alike just so he can do Conan's normal routine.
Later on in the episode, Kagura suddenly cosplays Yankumi, and mixes up lines from Gokusen and Trick.
In addition to that, the rest of the images also depict cutscenes from various Playstation era games, including a Metal Gear Solid codec sequence, the Opera scene from Parasite Eve and the scene where Squall sees Rinoa for the first time in Final Fantasy VIII.
In chapter 426, Gintoki is even cosplayed as Cloud because he is also carrying a big sword (an "alien slayer", according to him, a reference to manga series, Berserk).
Episode 204 has Gintoki asking "Is that your final answer?" And of course, it wouldn't be complete without Shinpachi going "Final answer! Wait, can I ask the audience?"
Episode 207-208 bears a striking resemblance to Kill Bill, including the music and naming of the assassin assassins.
Then in Chapter 362, Kyoshiro decide to change his shop to Plamo-kyo Shiro.
Not to mention, the spoof song of the original "Ai wo Torimodose", with lyrics "I AM SHOCK!"
The entire Renho arc is a shout out to Space Operas - particular with Gundams ("Even Bright-san had never hit me!").
Chapter 356 features the trump card weapon the Renho (Elizabeth's race) plan to use to invade Earth: the "white devil" mecha, which have blue color at the top, very blockish looking, and features beam saber and beam rifle - or as Shinpachi said, "It's not Renho army, that's Renpo Army!
Some people in 2ch even call this the only Gundam show this year.
 This video shows a visitor that was suspiciosly similar to Kai Shiden talking to a man that looked like General Revil talking about Katsura's exploits, only for the Not!Kai Shiden beating the hell out of Not!Revil for talking instead about the 30th anniversary of Gundam.
Of course, Fumiko is a complete shout out to Fujiko Mine.
Don't ask why Tama ended up in a Guntank body. All we know is she move faster this way and can detach her coreblock.
During the Tsusengumi Arc, Shinpachi and Hijikata play a card game with "Otsuu Cards" that is suspiciously like Yu-Gi-Oh!.
Episode 216 has some random Metal Gear shout-outs, with the "Patriots" being composed of the "naked" and "solid", which need to be "jacked" in with a stick. Gintoki also refers to strawberry milk as "Meso Gear".
Episode 217 has Gintoki trying so use Inception as an excuse to take a nap.
In one Popularity Ranking episode, Katsura and Otae try to goad Hijikata into saying one of Masamune's signature Engrish phrases and ask him if he's excited since SB was about to start its second season.
In chapter 363, Hijikata rides in on a nearly naked Kondo (who has motorcycle handlebars taped to his head like Masamune's horse in the anime) yelling "Here we go! Okay! Let's Party!"
Episode 228-229 (chapter 347 - 350) is an entire arc about Love Plus.
Chapter 372 begins the arc that deals with a villain who made himself the best friend of everyone in Kabukicho in place of Gin. Incidentally, the name of the arc, aside from being "Kintama", is also subtitled as "The Lost Substitute Odd Job Arc". Unlike other shout-outs, the arc is played with a more serious tone. (of course, being Gintama, the solution is still plenty of toilet humor).
In the first episodes with Hedoro, Gintoki pushes Kagura around in a wooden cart like Lone Wolf and Cub.
Chapter 403/Episode 262 introduces a former instructor of the Shimura family Dojo, Obi Hajime. His nickname is Obi-One. and not only that, the people who "saved him" and transformed him into a cyborg are reminiscent of Yoda as well.
The Stand arc in episodes 131-134 is a parody of JoJo's Bizarre Adventure, though, of course with Artistic License of some takes, though there are some real references such as the Star Platinum lookalike Star Silver, and the Rapid-Fire Fisticuffs in the battle between Okami and Gin. It's hilarious in hindsight now, too, since Tomokazu Sugita, Gintoki voiced Joseph Joestar (Battle Tendency, Part 2), as well.
There's also a reference to Hirohiko Araki as well, mentioning that he is a fairy (maybe discussing his memetic inverted age process) compared to the Gorilla of their author (Hideaki Sorachi).
Chapter 416 makes a huge shoutout to famous copywriter Shigesato Itoi and one of his most famous creations, Mother, when the Yorozuya is formulating a publicity poster. They use an image from the commercial for the first game as the basis for their poster initially (Along with its tagline), then randomly start putting pictures of Itoi himself on the poster, as well.
The arc between chapters 233-236 plays a huge reference to Saw when Hijikata & Okita are chained in a room by a man with a mask called Jiguzou and both of them have to prove the strong bonds that they have... but it proves to be a stunt set by Okita to get rid off Hijikata.
Fullmetal Alchemist is referenced, even with the transmutation circle and quotes in episode 69.
At the beginning of episode 183, the opening of Fist of the North Star is parodied. The music and the setting was reused in the second movie.
Chapter 420 brings us Umibouzu and Gintoki dressed in HUGE ADULT bodies, based on Yoichi Takahashi's drawing style of Captain Tsubasa's fame.
The many, MANY references to B'z, one could assume that it's one of Tae's favorite (Real World) j-music bands... but even Kagura has referred to them in ocassions (even the in-world reason of the formation of the band: Two sorcerers fighting a demon with lyrics as spells. 'Bad Communication' indeed...)
Not only them, but TOKIO has also been mentioned a pair of times. And also people from Johnny's Jimusho agency.
And Perfume isn't saved at all either - the unit that Tae, Kyuubei, Saachan and Tsukuyo form in the Popularity Poll arc are named "Diamond Perfume", who came back during the HDZ 48 arc.
In the arc of the Galactic Idols, mentions about AKB48 are also valid, especially since Otsu seems to be losing popularity by herself as an Idol Singer than, being in an unit like this one... besides the whole fact that she has to fight the top galactic unit of 'idols', GKB48.
In the second movie, Otsu have joined Oedo Muscats, a parody of Ebisu Muscats, which compose of AV actress and gravure idols, and shot videos for SUTEKI - considering it's a parody of Muteki, it's extremely likely to be an AV video. Meanwhile Gin was concerned that Yorozura broke up just like The Checkers and worried that one of the two had wrote an "autobiography" to smear the other one.
Chapter 436 brings up the Burakkumas. Plainly rip-offs of Rilakkuma intended to be a set-up trap from Tae for Katsuo, as being part of the new generation of the Four Devas to 'clean up' the bad influences on Kabukichou.
In the Diviner arc, Gintoki's balls have individual names: Yusuke and Sasuke. Mind you, that they are meaningful names (Yusuke being for 'Right Hand' and Sasuke for 'Left Hand') BUT, they are also indeed Sket Dance references too (AND spoilerish, by the time this chapter was published, it was revealed that Bossun aka Yusuke and Tsubaki aka Sasuke were twin brothers). That is, also because Kenta Shinohara was an assistant of Hideaki Sorachi for a time before creating his series.
In one of the Next Episode Preview of the Gintama' Enchousen season, the Yorozuya jokes around about making a parody of Kuroko No Basuke. Some months later, in the recent arc of the Party Reunion (and a bit hinted at the end of the Gintama: The Final Chapter: Be Forever, Yorozuya, which was directly written by Sorachi himself) we get to know about the Miracle Generation of the Joui War, conformed by Gintoki, Katsura, Sakamoto and Takasugi... and about a fifth 'Phantom' member of name Kuroko no Tasuke.
Not so much longer after that, To Love-Ru is even mentioned (and compared to Gintoki's "old days of Jump" when Is was published, sort of generation thing between his and Shinpachi's manga soft-porn) and Saint Seiya is also referred. Cue to Gintoki's "fear" of being sued just because it was three series parodied and referred in a row from Weekly Shonen Jump's past and present authors.
The second part of gambling episode, where Kada is being introduced, is the whole Akagi series, concentrated. It's all about mahjong, naturally. "ZAWA!"
Thanks to Hijikata-in-Gin's body, from Chapter 471 to 473 Shinpachi, Kagura, and a bunch others became like Saito Hajime from Rurouni Kenshin, complete with strict hairstyle and his signature style/attack, the Gatotsu.note Considering that Saito was based in another historical Shinsemgumi member, and that Hijikata was trying to become stricter with the Yorozuya.
Sougo dressed up like Kenshin in the second movie.
The names of four Kyubei's bodyguards (including their leader, Tojo) are based on the names of the four main girls in Strawberry 100%.
Chapter 486 becomes a huge Street Fighter parody once Shinpachi starts trying to use his dojo's secret technique (Which had its instructions written as a fighting game command). Among other things, it has Kyuubey using Guile's Flash Kick, and displays a parody of the results screen from Street Fighter II whenever Shinpachi tries and fails to use the technique against his opponent.