Pet Shop of Horrors/WMG

Leon was killed by D before he settled in Japan
It would certainly explain why he ceased being mentioned, or appearing at the end of sidestories in Shin Pet Shop of Horrors. It would also give us a very grim reason for Leon not returning to America in order to be with Chris in twenty years.
 * For those who wish to call upon the framed drawing that Chris made (of D, Leon, some pets and himself), it could mean that Leon framed it and kept it at home, or that D went ahead and took it from him, either framed or unframed, before or after he killed Leon (remember how he defended his suitcase, where he had the drawing? It's important for him!)

And why killed, you say? Because Leon did catch up with D eventually, after the Germany and Italy sidestories.
 * Hey, just noticed! Germany-Italy-Japan!

D is the product of his father's research, just like Howell said
Makes more sense to have the family's only surviving ancestor split in two (Sofu and Dee), in order to handle the memories and emotions (anger, pain, fright) better. They could have the ability to be reborn upon dying (Dee did it), as well as longevity and eternal youth. This would account for all the other Counts that don't look like either of the current three, and would put Dee as the one Chris meets at the end of PSOH (respecting the most common Epileptic Trees on the issue).

The D we all know and love, though, could only be Dee's creation when he learned enough about genetics and stuff; probably a backup plan for his eventual suicide when reborn as a human (Dee is long held, both in Fanon and Canon, to be insane; he could have been driven to insanity and death by the emotions of his "ancestor"). This experiment angered Sofu (the most likely host of the "ancestor's" memories, given that he knows the story the best), who took the new D with him in order to raise him... before he was complete, as his mysterious illness and eventual cure (that poor orangutan) seem to imply. For building D up, Dee could have taken part of his "father" (Sofu) and part of himself, therefore giving D his odd eyes. D is probably the most close in appearance to their "ancestor", if this holds true.

Lastly, the terms father for Dee and grandfather for Sofu could be there only for formality. After all, Dee is the closest thing D has to a parent, and Sofu most probably wanted to rule over them both somehow (telling D all his life he was his grandfather, to inspire respect and authority... and probably discredit his "son" Dee).

The Pet Shop of Horrors universe is an alternate reality of a world with a superhero or superheroes
Take a look at the setting: a major American city with lots of crazy and interesting crime. Take a look at the recurring cast: a Hot Blooded cop, his pretty female partner, his cute little brother, Da Chief, and an enigmatic Stepford Smiler with a certain distaste for humanity and mad kung fu.

Now think about it: in any other story with magic and serialized installments, wouldn't D be the villain, no ifs, ands or buts? Instead, the punishments he metes out are tolerated, if not exactly liked, by pretty much everyone but Leon, the one clean cop in town. Hm, now what does that sound like?

Perhaps  makes a hobby of killing off capes (and considering how often human arrogance is amplified in supers, he almost certainly would want to); perhaps the   were meant to be the forerunners of the superhumans but ended up being forerunners of  ; or, as stated in the above title, perhaps this all takes place in a Wonderful Life universe.

In 'real' continuity, The Hero is most likely Blue Oni to Leon's Red and has many Shut UP, Hannibal moments when fighting D.
 * ... Are you suggesting a Watchmen/Pet Shop of Horrors crossover?
 * Someone needs to write this. Either of them, crossover or not. Now I want to know who this mysterious Blue Oni is!

The Ds are Merovingians
"It was believed that the blood in their veins gave them magical powers; they could make the crops grow by walking across the fields, they could interpret bird-song and the calls of wild beasts...

~ Martin Kitchen, Cambridge Illustrated History of Germany"

'Nuff said.

'D' stands for Dionysus
Just take a gander at this.
 * That would explain the craziness and anti-humanness, as Dionysos is the personification of unbound, wild nature- in contrast to Demeter (again a D!), who stands for civilized nature; nature overcome by man (like harvesting).

The series is unoffical continuation of Gremlins
Obvious, isn't it? A mysterious shop in New York Chinatown, selling creatures that have strange, supernatural conditions attached to them, that will cause disaster when broken. Count D even speaks of his grandfather who supposedly owns the shop, who is undoubtedly none other than the Chinese man in Gremlins. Count D may be an ursuper rather than an actual grandchild though, and obviously has exactly the opposite philosophy concerning the shop's creatures to the original owner, who only wanted to keep them, and prevent them from falling into hands of people who couldn't hold the contracts - Count D on the other hand revels in chances to give his animals to such unsuspecting clients.

Mustafa was purchased from D's shop.
Hence Kajika's haste in coming to the conclusion that Eugene is her pet leopard returned to life.

Shin Pet Shop of Horrors is actually a prequel to Pet Shop of Horrors.
Thus why D has suddenly lost ten volumes' worth of character development. We just have it confused because of the side stories involving Leon. That's also why they stopped after two installments -- the author realized that it was confusing people.

Count D is a Time Lord.
You all knew this would come up eventually. As for his TARDIS, it's obviously the Pet Shop, which has been stated by almost all characters who have gone into the back rooms to be far bigger on the inside than it looks on the outside.
 * Shout Out?
 * In volume 8, it is heavily implied explicitly stated that he went back in time to rescue Peggy Greenberg.
 * People constantly confuses him with his father and grandfather. There is no "father" or "grandfather"- this is just a ruse. He's really been alive and operating the shop for almost a hundred years.