In one chapter of the Bobobobo Bobobo manga, Yugi Mutoh from Yu-Gi-Oh pops out of Bo-bobo's afro and summons Sky Dragon Osiris (AKA Sleifer the Sky Dragon) to help battle Halekulani.
Naruto on Ben 10
Naruto in South Park. (in one instance a guy is talking about about how to solve your childs A.D.D problem. And behind him sitting at a desk, you see a kid with blonde spiky hair, a blue head band and a light orange jacket with the blue parts around the shoulders.)
Super Saiyan in Codename Kids Next Door.
Super Saiyans in Grim adventures of Billy and Mandy.
Goku and Gohen from DBZ show up in Robot Chicken episode called Chickenball Z
Ranma episode 28 - Ataru Moroboshi of Urusei Yatsura makes a cameo in this episode. When Shampoo turns a dog into a man, the man that dog turns into is Ataru.
In Project A Ko, it's hinted a few times that Eiko's parents are Superman and Wonder Woman, though they've never appeared onscreen in costume. (Although they have appeared with costume -- Mrs. Magami is shown sewing or repairing a Superman outfit at one point.)
An episode of Full Metal Panic:Fumoffu had a gangster referring to 'Ambassador Ma
In episode 21 of Keroro Gunsou, thinly-disguised versions of Lupin III and Jigen get run off the road by the Hinata family car in an obvious parody of a scene from The Castle Of Cagliostro. In episode 48, there is an inexplicable appearance by a human-sized version of the giant floating Rei Ayanami from End of Evangelion.
Cromartie High School - Dejiko, Puchiko and Piyoko from the anime Di Gi Charat make several cameos in the anime.
Comic Party has cameos from the characters in To Heart.
Anime called Air - In episode 2, After Yukito tells Potato to wait in the bushes, he asks 3 girls where Kano is, the 3 girls are Ayu, Nayuki, and Makoto from Kanon.
Star Trek has a lot of Anime references. Ships are named after Kei and Yuri from Dirty Pair. In one episode there's a calligraphy of background scrolls that spell out the names of Urusei Yatsura's main characters.
Soul to Seoul Manga volume 1: Spike Spiegel and Faye Valentine from Cowboy Bebop in a crowd scene.
Robot Carnival anime: a very quick cameo by Tetsuo and Akira from Ohtomo's manga as they quickly walk out of the theme park at the beginning of the story.
Detective Conan cameo in Inuyasha is in episode 128.
Miss Hinako, Ranma, and Akane watch an episode of Doraemon in Volume 30 of the manga.
The following were found by someone else. I just happen to find a text document with them in my documents but I don't know where it was from I had saved it on April 5, 2003 though.
Original Dragonball movie 3 featured Son Goku and Tao Pai Pai fighting in Penguin Village and running into Arale of Akira Toriyama`s other popular series Dr. Slump.
Geobreeders featured a cameo by Kyoko and the Akie`s family restaurant from Cat Girl Nuku-Nuku. (Both Geobreeders and Bannou Bunka Neko Musume were directed by Yuji Moriyama.)
Sawa of Kite has a walk-by cameo appearance in Yasuomi Umetsu`s latest OAV Mezzo Forte.
Fred Ro of Outlaw Star had a walk-by cameo in the first episode of Angel Links. Valria and Douzu appear briefly in Outlaw Star as well, and become main characters in Angel Links.
Tokyo Babylon`s Seishirou and Subaru both appear in the beginning of the X movie.
The short CLAMP anime music video CLAMP in Wonderland features numerous CLAMP titles all interacting, including Rayearth, X, Tokyo Babylon, RG Veda and Clamp Campus Detectives.
Dirty Pair TV episode 26 features very quick little parody cameos by Ataru Moroboshi and Lum from Urusei Yatsura.
In El Hazard: The Wanderers you see magical girl Pretty Sammy show up on posters once or twice, and Jinnai is reading a Tenchi manga in a flashback as well as having a spy bug named Tenchi. In Tenchi in Tokyo Mr. Fujisawa is one of Tenchi`s teachers. During a field trip when Tenchi and his friends fall into a pit at a historical dig site, Fujisawa wonders if they might have fallen into "the magnificent world (El Hazard)." For the most part those are the most noticeable ones. There are others, but they tend to be just a case of name dropping.
The Dirty Pair make their first ever animated appearance as the stars of a drive-in movie in the Crusher Joe movie.
The biggest example of crossovers goes to Leiji Matsumoto who has weaved the entire "Eternal Traveler" concept through Captain Harlock, Galaxy Express 999 and now Yamato.
Yawara and Jigoro from Yawara! make a quick cameo in Project A-Ko 3.
One of the best examples of a crossover is Scramble Wars, the second part of AnimEigo`s Super Deformed Double Feature. It features several different Artmic characters from Bubblegum Crisis, Genesis Survivor Gaiarth, and Gall Force.
Rio and Yuji from Burn-Up W have a walk-by cameo appearance near the end of Tenchi in Tokyo.
The Daicon 3 & 4 opening animation sequences aren`t really valid entries because they were non-professional, unlicensed, fan-produced shorts, but they do deserve mention because they were produced by the people that would later form Gainax Studio, and feature literally hundreds of cameos ranging from anime to Ultraman to Star Wars.
In the first Tenchi TV series, the Washu robot with Mihoshi`s brain watches Moldiver on TV.
The Dirty Pair return the favor in Project Eden: Crusher Joe appears on a video screen in the Lovely Angel ship while Mughi`s flipping channels.
Misa Hayase/Lisa Hayes appears in a "RATS" style erotic flashback in Orguss.
Rumiko Takahashi has numerous cameos in her series. Lum and Ran appear (in chibi form) at a festival in Maison Ikkoku. Yotsuya-san makes a reference to watching UY videos in one MI episode. Also in UY episode 46, "Lunch is a Battlefield!" Kyoko-san`s father-in-law and Ikuko-chan are sitting at a sidewalk cafe when the gang goes running by.
In Shin Cutey Honey OAV 5, Akira from Devilman assists Cutey Honey.
Tezuka Osamu had frequent cameos of his numerous characters show up in series other than their own, especially in his manga. As someone fascinated with the world of cinema and the musical stage, he seems to have thought of his characters as a sort of "stable" of actors and would occasionally bring them into various stories, sometimes in uncharacteristic roles. As one example, Higeoyaji (whom Americans generally know as Mr. Pompus) turns up in a lot of other anime and manga titles besides Tetsuwan Atomu; Hamuegu (Hamegg) and Asechurin-rampu (Acetyline Lamp) are sort of stock villains that Tezuka used widely as well. And in the anime movie "Marine Express," a number of the characters from Atomu appear in alternative roles.
In the Silent Mobius TV episode "Mobius Klein," Assembler from Kia Asamiya`s Compiler series makes a cameo talking to Katsumi`s Mother.