I personally believe that,
Muffintop (and other food based Phobies), could be based on Cibophobia, or the fear of food.
Henrietta is Arachnophobia, or fear of spiders.
Bo Mangles is Coulrophobia, or fear of clowns.
K-9000 and Cerberus could be Cynophobia, or fear if dogs.
Doctor Dermic could be several, including fear of needles, Aichmophobia, or the fear of doctors, Iatrophobia. But I thing Trypanophobia, or the fear of injections, works best.
Fears of germs, diseases, and bacteria fit Gesundheit and Mike Roscopic very well. ( mike could also be the fear of small things)
Jack & Jill could be Gamophobia, or the fear of marriage.
Murderwing, Eternal Knight, and Gravedigger could be Necrophobia, or the fear of death.
Misanthrope could be fear of people, Anthrophobia.
I also have noticed several sharks, a common fear as well, or eve repersenting Hydrophobia.