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Though it never crossed over with both at the same time, It's Walky!! had crossovers with both Melonpool and Fans!! that established both as part of its universe (or multiverse in the latter case) and which ended up having a lasting impact on its storyline.
Kevin & Kell and General Protection Fault had an arc where two GPF characters wandered into K&K's Domain world. The artists managed to work the events into both their storylines that were running at the time, and apparently drew a strip each day—both had two-strip days where the storyline advanced.
Starslip Crisis: Alterverse War is a mashup of a large number of science fiction webcomics, and had just started as of October 2007.
Questionable Content has crossed over with Diesel Sweeties, which has itself crossed over with Scary Go Round. Questionable Content has also crossed over with Applegeeks, which, having crossed over with Ctrl+Alt+Del, would turn the whole group into one quasi-incestuous ball of webcomics. I'm reasonably certain that PvP has been referenced in at least one of these, probably Diesel Sweeties, and since the former has crossed over with Penny Arcade more than once, it's completely cross-eyed insane over there.
And the Author of Ctrl+Alt+Del exists as a person in the Penny Arcade universe, so that means, if you follow the little red thread of universal strings, that he exists in the same plane of existence as his characters..
Don't forget that Applegeeks had a major crossover (well, on its end) with MegaTokyo at one point. Which chains the whole thing to a specific date, making things even crazier.
The cast of Shortpacked has visited the Coffee of Doom coffee house from QC on occasion, including once when both artists did a take on the samescene. Combine that with the S*P Intercontinuity Crossover Nexus mentioned above, along with all their respective crossovers, and we have a massive webcomic universe that could give Marvel a run for its money.
Several members of the "Webcomics Inc." social networking site collaborated on a crossover comic, where they made all their characters teen-aged and put them into high school together. The result, "WCI High", merged characters from "Good Times", "Mikey's Life", "Everyday Heroes", and "Big Sandy Gilmore". (Of these, only Everyday Heroes seems to be still actively updating.)
Least I Could Do recently finished the Ultimate Final Civil War Invasion Crisis Thing, which featured the gaming webcomic characters trying to kill the slice-of-life comic characters. (Cyanide and Happiness, meet xkcd.)
Ménage à 3 and Sore Thumbs crossed over at some point and are implied to be in the same universe, and Ménage à 3 crossed over with School Bites. If this keeps up we'll wind up with every webcomic crossing over to one another.
The writer of No Rest for the Wicked footnotes her comics so you can get all the fairy tales she's using characters from.