Er... I'm thinking I might not have understood your question, or maybe our undergrad programs were different, but I had a course titled "Microbiology". 🙂
That said, my VMCAS page doesn't have a "microbiology" option in the list of prereq designations (I've got biochem and genetics, but not micro). Maybe that's because I didn't designate any schools that require micro, and the system is smart enough to only list prereqs for schools you said you're applying to? That would be pretty annoying since I'm not really done deciding where I'll apply, and it would suck to have to re-do all my prereq designations at the last minute...
EDIT: Oh, duh... After reading OceanAngel's response, I realize that I interpreted your sentence backward. I thought you were saying there was a category called "microbiology" and you didn't know what course(s) to use to fill that... When in fact you were saying you'd taken microbiology and didn't know what category to assign it. Yeah, I labeled my micro course as "biology" too. 😳
I think I am probably putting it under Biology because a lot of the schools I have noticed include microbiology under their list of possible biology courses to fill the prereq. I guess you could also put it under "other" if you have schools specifically asking for this prereq, it's just too bad they don't let you distinguish what "other" means!