The Funky crossover that just happened also involved John Darling, actually…his grown-up daughter is engaged to the son Lisa gave up for adoption, which is why all of the backstory was going on. Batiuk has changed Lisa’s story, too…apparently she was now raped and got pregnant with that son instead of it being a voluntary, if bad, decision. Which, again, was what this recent crossover was all about. Apparently Jeff and Pam found her right afterward and got her medical attention.
R. K. Millholland of Something Positive fame used to do crossovers with Aeire of Queen of Wands. When she ended the strip, he adopted Kestrel, her heroine, as one of the characters in his universe. Lately, he’s been doing crossovers with Danielle Corsetto of Girls With Slingshots.
Jeph Jacques of Questionable Content hasn’t done crossovers per se, but he has lots of guest artists and sometimes borrows their characters for one-offs.
Also, Dave Willis’s Shortpacked! One of Willis’s recurring characters (after a fashion), Singularikitty, is one of the offspring of Choo Choo Bear and…ach, whatever the female from GWS is called.
Both SP! and SP have crossed over with T Campbell’s strips - SP! had a major crossover with Fans, and Davan befriended Penny and Aggie’s Helen, who migrated to SP a few months before P&A ended. (And eventually had her storyline go on indefinite hiatus. Milholland claims because he finds her story too depressing - how badly, and aggressively, must she be screwing up her life to be more depressing than Kharisma?) (Since Fans and P&A are explicitly in different, alternate universes, this leads to a bit of a logical problem. That can be solved by simply - LOOK OVER THERE!!!)
There was also a sort-of-crossover between P&A and Menage a 3 (written and drawn by P&A’s original artist, Giz), where Lisa and Stan from P&A went to Montreal (for some reason), and Stan got kicked in the balls by Ma3’s resident phallophobe, Yuki. (He no doubt did something to deserve it, but Yuki was on a ball-kicking rampage at the time.) (This is of dubious canonicity for P&A.)
A major arc of P&A also included a brief cameo by one of the main characters of Giz’s previous comic, Cool Cat Studios.
T’s crossed over several of his comics in various ways - alternate versions of characters from one will appear in another, as well as a P&A filler arc set in the Fans universe.
Lio gives FBoFW a well-deserved stick in the eye.
Lio takes on the glacial growth of the comics page.
That was all more or less “implied”, since to make any direct references to anything Batman would involve coordination (and money changing hands) between TMS (DT’s syndicator) and the copyright holders for Batman.
That said, the Daddy Warbucks’ appearance was very easy to do since TMS owns the rights to both “Dick Tracy” and “Annie”.
That would be DC comics, which is a division of Warner Brothers.