All of the shows by AIC makers of Tenchi Muyo! crossover some what with each other Dual! ended up with an cameo and recycling the "Light hawk wings" for its big mech. later in Tenchi Muyo! GXP and mech looking like the one from DUEL! showed up in an episode.
In one episode of the 1980s Astroboy, the titular robot is taken back in time, along with his sister Uran, the one and only Black Jack and the doctor's assistant/companion Pinoko, in order to save the main character from ''Princess Knight. Good ol' Tezuka mix-and-match.
The mangaka group CLAMP have crossed their works over to the point that now they are all in one big, weird world. Some of these are significant to the plot, many seem to be just for fun. A frequent crossover element is the Clamp Campus, a gigantic private school that shows up in CLAMP Campus Detectives, X/1999, Dukylon: CLAMP Defenders, and Man of Many Faces. Characters from Chobits make an appearance in Kobato. The protagonist of Tokyo Babylon, Sumeragi Subaru, shows up in X/1999. Even their "joke" series Miyuki-chan in Wonderland contains crossovers. In one story, Miyuki ends up as the Damsel In Distress in X/1999. In another, she ends up playing (strip) Mahjong with other characters from CLAMP works. And there are the tribute music videos CLAMP in Wonderland and CLAMP in Wonderland 2 which have segues between all of their series to date.
Then there is Tsubasa Reservoir Chronicle. The entire basic premise is being an Alternate UniverseMassive Multiplayer Crossover with characters from most of CLAMP's works showing up, often in different contexts from their original portrayal, such as characters from opposing sides of X/1999 hanging around the same cafe. Two of the main characters are alternate versions of the main characters from Cardcaptor Sakura. AND it is the sister series to Xxx Ho Lic. The plots of the two series are so intertwined that they are essentially two vantage points on the same story.
In the manga Digimon V-Tamer 01 are a total of 3 non canon crossovers, each being about a hero of the current digimon anime series being space warped and ending up battling an extremely powerful digimon together with Taichi and Zero.
The authors of Fairy Tail and Flunk Punk Rumble did a one-shot called Fairy Megane that brought together the main characters from the two series. (The mangaka of the latter used to work as an assistant to the mangaka of the former.)
Likewise Fairy Tail crossed over with Rave Master, the previous manga series of the author.
Go Nagai has frequently crossed their different works (mainly his Humongous Mecha series) over since the seventies. Some of the main instances are:
Mazinger Z, Great Mazinger, UFO Robo Grendizer, Getter Robo, Getter Robo G, Devilman and Cutey Honey in the Dynamic Heroes e-manga (also known as Nagai Go Manga Gaiden - Dynamic Heroes or Go Nagai manga heroes crossover collection - Dynamic Heroes), an e-manga released in 2004 and later compiled in tankoubon.
Getter Robo and Devilman in the "Devilman vs Getter Robo" manga. At the end of it, Akira and Miki lampshade the trope, joking about whom they will visit the next time.
Leiji Matsumoto's works. Like with CLAMP everything is in the same universe (Yamato and Harlock and Maetel and Emeraldas and the Queen Millennium...) but details do not match (Tenshiro died in three different ways already).
There are also separate anime and manga crossover specials of Toriko and One Piece.
And now there is going to be an OVA crossover with all three.
One Piece and Toriko have crossed over three times so far, the first special (which was animated) took place pre-Timeskip in One Piece, while the other two take place post. Both authors are real good friends so theres a chance that the crosses are canon.
Pretty Cure All Stars crosses over all the existing Pretty Cure series in one big movie. This has gone from one movie teaming four teams to five movies featuring eight teams.
In honor of Shounen Sunday's 50th anniversary, the publisher released a DVD including three OVAs for their three most popular animes: InuYasha, Urusei Yatsura, and Ranma ½. The DVD also included this animated short, where the main characters of the three series met up. Hilarity Ensues.
Turn A Gundam acts as one for all of the Gundam shows that came before it. Universal Century mobile suits are excavated and used by the protagonists while newer mobile suits use technology from Universal Century. And near the end of the series, the Black History is revealed to be every single Gundam series, both before and after Turn A.