These were on Webcomics Multiverses, which was determined to be kind of redundant. Leaving them here for posterity:

• Air Force Blues presumably shares the same universe as Box D Blues and Air Force Toons, the former a webcomic, the latter a newspaper comic, both done by the same author. While Air Force Blues follows a group of Air Force pilots stationed in Alaska, Box D Blues and Air Force Toons both follow enlisted airmen stationed at different bases.
  • Meanwhile, Air Force Blues and Crew Dogs both did lengthy crossovers every few years, establishing that they were all in the same universe, just taking place at different bases. PVT Murphy's Law, another newspaper comic, also did a brief crossover with Air Force Blues
• Bobbinsverse: Bobbins, Scary Go Round, Bad Machinery. Crossovers: Goats, Superosity.
• Crew Dogs, as mentioned above, shared a universe with Air Force Blues.
• Cyantia: Satin & Silk, Campus Safari, No Angel, Shivae!, Akaelae
• Girlyverse: Cutewendy, itself a variation on earlier comic Wendy, segues into Girly, which also features Wendy characters. Doctor Voluptua apparently takes place in the same world.
• Gonter Verse: Pretty much everything David Gonterman has ever made, depending on his mood.
• Furryverse: A lot of furry webcomics share characters; the character Zig Zag, most famous in her role in Sabrina Online, gets around.

• Jenniverse: Unicorn Jelly, Pastel Defender Heliotrope, To Save Her
• Megageekverse: Megatokyo and Applegeeks. A noted crossover between two authors.
• Furthermore, Applegeeks has done several crossovers with Ctrl Alt Del, but Ctrl Alt Del hasn't appeared in any Megatokyo comics.
• ND Unlimited: Unlike Minerva, Namir Deiter, You Say It First. The non-anthropomorphic series by Terrence and Isabel Marks (Spare Parts, Undoubtedly Kawaii, The Shokora Diaries, Girichoko's Story) are fictional stories in that universe, and vice versa.
• Narboniverse: Shaenon Garrity's Narbonic, Li'l Mell, Skin Horse.
  • Skin Horse is confirmed to be in the Narboniverse, and Smithson might be included by virtue of the appearance of Homeschool Joe from Li'l Mell.
  • The core cast of Webcomic/Narbonic made a cameo appearance in Everyday Heroes, and Caliban has also shown up a few times. This probably isn't enough to consider the latter as part of the Narboniverse.
  • Shana from Fans gets kidnapped by a mad science convention in Narbonic. Later, the original Helen Narbon appears in Fans.
• Overside: All of Evan Dahm's comics are set here—Rice Boy, Order Of Tales, Vattu, and a number of short stories.
• Roomieverse: College Roomies From Hell, UC Rats, the comic series version of Tangents (there were several 'Maritza's Minions' series, most of which lasted less than a year)
• Shmorkyverse: Living In Greytown, Lizard (as much as the author would like us to forget these)
• Somethingverse: Something Positive / Something Positive 1938 / Midnight Macabre, Queen Of Wands / Punch 'an Pie, Girls With Slingshots, Penny And Aggie, Cool Cat Studio, Sketchies, and possibly, by extension, Alternate Universe versions of the Fans, Clan Of The Cats, Questionable Content, College Roomies From Hell, and the inhabitants of the Walky Verse and Melonpool. There's a possible case for including Alternate Universe Sluggy Freelance characters as well. One of the few shared worlds by two or more authors.
  • This may be growing, like a strange and beautiful Myth Arc, to incorporate several of these other Verses into one Gestalt Webcomic verse.
  • Argumentatively, could be a larger Topatocoverse (after the company), with the Wiguverse, xkcd, Dresden Codak, and even Little Gamers thrown in for good measure.
• Walky Verse: Roomies, It's Walky!, Shortpacked, Joyce and Walky!. Crossovers: Melonpool, Fans.
  • Don't forget Questionable Content, when the Shortpacked! staff visited "Coffee of Doom", see (here) and (here), also done in a more subtle way (here)
    • Which is really weird, considering QC takes place in Massachusetts and Shortpacked is in San Francisco. That's a long way to go for coffee (and snark).
  • And Shortpacked! has joined the Something Positive/Girls With Slingshots crossover, with Leslie adopting one of Sprinkles and Choo-Choo Bear's boneless mutant kittens.
  • And now it's crossing with Multiplex.
  • Dumbing Of Age is an Alternate Continuity of Walky Verse characters, without the alien stuff. Life Unembellished, as it were. (If it crosses over with just about any of the strips mentioned in the five preceding paragraphs, we could have some sort of multiverse-ending continuity snarl. ...Which might be fun to watch!...)
• Wotchiverse: The Wotch, Cheer!, Triquetra Cats (arguably Zebra Girl, Accidental Centaurs and Abstract Gender as well, but most emphatically not El Goonish Shive, no matter how much the fans of both bitch about it.)
  • El Goonish Shive does take place in a multiverse however; its just that the entire multiverse exists within the canon of the one webcomic instead of being shared with other webcomics. Crossovers do take place in the guest comics though.
• Wiguverse: When I Grow Up, Wigu, Wigu Adventures. Crossovers: Overcompensating.
• Ultima-Java originally had a Multiverse in place, but has since January 2010, the concept has been removed, compressing all it's alternate coninuities into the UJ-verse. However Ultima-Java still hosts the pre-reboot continuty comic, that has been dubbed Universe 2 in reference to the DC Golden Age originally taking place on Earth 2. Ultima-Java also hosts other comics, that do not take place within the UJ-verse.
• The webcomic hosting site Drunk Duck has a peculiar version of this, in that all webcomics hosted on the site apparently share a universe, as demonstrated by the myriad crossovers reminiscent of Marvel. And for some reason, the authors of the comics are included in the universe.
  • Perhaps not every one, but definitely most of the superhero comics.
    • For a while, nearly the entire site was part of the "Drunk Duck Civil War", which was, obviously, a parody of Marvel's Civil War. However, the most notable example of this trope is present in Fightsplosion, a tournament hosted on the forums where contestants battle it out in duels and the winner is chosen by reader vote. The matches are chronicled here: http://www.drunkduck.com/Fightsplosion_Legends/index.php
• Rival webcomic hosting site Comic Genesis has been known to randomly generate "Jams" on its forums. These Jams feature forum regulars as the characters, and generally consist of one of the forumites posting a part of the "story" (which rarely proves consistent or understandable), followed by a different forumite, and so on and so forth. The process is very casual and has produced a good portion of the in-jokes of the forums there. The Jams are chronicled (occasionally) at http://spacejams.comicgenesis.com/
• The recent Crossover Wars linked a large number of otherwise entirely unrelated webcomics together. How much impact on functioning Canon the Wars had varies from comic to comic, however, so they can be considered part of the same multiverse only in the throes of WMG.
  • Then you have the spinoff The Crossoverlord which has tons of cameos from other webcomics all over the place. The comic's website even has a list of separate realities connecting various comics together (link). Like Crossover Wars, how the affect the various comics' canons varies.
• The Vefurrin and HERO universe — the main character of the former, Ganymar, appears as a significant side character in the latter, and Word Of God says that the two tales indeed take place in the same universe. Of course, given the seemingly strange and shifting nature of said universe, that really wouldn't be much of a stretch in any case.
• The Dieselverse: R. Stevens' Diesel Sweeties and Lolbots. However, Word Of God (via e-mail correspondance) considers the latter strip's characters to either be younger, or the strip itself to be Alternate Continuity. (Also, the strips' Red Robot uses the same chassis as Exploding Dog's Red Robot).

• The Jet Dream Universe: The "TG Comics" titles Jet Dream, It's Cookie!, and My Jet Dream Romance take place in the same universe and share the same fictional publisher.

• Project Future is set in the future (~150 yr) of Dan And Mabs Furry Adventures.
• Mortifer and Evil Plan have had a couple crossovers, as have the artists' other works, Fringe Happy and Sire. Also, since Piper appears in both Mortifer and Fringe Happy, we can assume that those two take place in the same universe, as well.
• The International Comic Continuity consists of nineteen Sprite Comic series by fifteen different authors that decided to combine their pre-existing series into one universe.

• The Shineverse comprises both the main comic and its self-contained spinoff The Eagle of Hermes.
• All Over The House shares a multiverse with The Life Of Nob T Mouse. In addition, The Life Of Nob T Mouse has its own internal multiverse, because Nob Mouse and friends redefined time using magic, creating "quantum history", so now every point in time is a separate universe.

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Does the pixarverse qualify? Elements from Toy Story 1,2,3, bug's life, monsters inc, wall-e and others all appear in each other, including some characters (like Wall'e and Hugsalot)

This is just a mess:

• Final Fantasy XII, its sequel Revenant Wings, Final Fantasy Tactics, Final Fantasy Tactics Advace and Final Fantasy Tactics A2 (The latter two primarily due to character overlap) and Vagrant Story all take place within the world of Ivalice.
• "The Compilation of Final Fantasy VII". And Squeenix is trying to emulate that success with the "Fabula Nova Crystallis" project.
  • The above Final Fantasy examples are actually examples of a multiverse spanning the entire Final Fantasy series.
    • And there is also the ending of the sequel to Final Fantasy IV where the last boss is the Creator goddess who apparently made both the worlds of Final Fantasy I and Final Fantasy IV as well as having the power to summon creatures from the other Nintendo-era FF Games.
    • Don't forget that hints have been dropped by writer Nojima that Final Fantasy X and Final Fantasy VII are connected, with the former happening thousands of years after the latter. And these examples haven't even touched on things like the Final Fantasy II and Final Fantasy IV dragoon parallels or Gilgamesh of Final Fantasy V being a dimensional traveler.
    • Oddly, Final Fantasy X-2 seems to imply that the latter happens thousands of years after the former. Either there's a compendium error somewhere or quantum physics is even squishier in the world of Squeenix than aforethought.