Ok, I just watched Season 1, the first two episodes of Season 2, and then read this whole thread. I admit as much as I love the character of Batman that I don't really read D.C. outside of a few books here and there, so I don't know much about Gotham. Having said that, I enjoy the show. I find it entertaining watching the characters origins, especially Jerome's.
This thread talks so much about the show and not nearly enough about Minimates.
My guesses:
Box set 3
Bullock
Falcone
Zsasz
Barbara
Box set 4
Fish
Butch
Maroni
Jerome