I have a dog w/ fear based aggression (diagnosed by U Penn's veterinary school).
We have him on a low dose of daily Prozac. It has taken time but we've learned his triggers. He's worse with barriers present (being on a leash, being restrained in some way, seeing a dog through a fence vs. in the open).
not the easiest thing to work on. We eventually, after much searching, found a trainer that specializes in fear aggression. She actually held socialization classes for special needs doggies. it was awesome and incredibly helpful for him. We basically set him up for success by learning to read his signals. She'd have us introduce the dog in a particular way so that it was far enough away that his stress level wasn't terribly high. We basically gradually worked on reducing that distance so he was more comfortable with the dogs increasingly closer. Of course, it is hard to find willing participants in the real world for such a thing, but maybe you can find a trainer like this.
We also did clicker training w/ him (look into Karen Pryor's work). Really helpful. We did things like standing outside of Petsmart and similar, but at a distance that we weren't very close to the dogs going inside. Far enough that he wasn't super stressed, but close enough he could see them. Basically we worked on feeding him treats and letting him build good associations w/ other animals. Having him on a low dose of prozac was helpful IMO in that it was enough to take just a bit of the edge off for him.
It is really hard. Now we have two kids and have moved away (out of state) from the trainer that we adored, so we aren't getting to continue to work on this stuff as much. I think trainers like her are tough to come by. We drove an hour away to see her, but she was amazing. We did a bunch of private sessions w/ her, and she did the "socialization class" for special needs pups for free on her own in the evenings, which was incredibly generous and helpful for those of us w/ rescue dogs w/ issues.