In Rochester, NY, it's The Distillery, on Mt. Hope Avenue (1650 Mt. Hope, I think). Pretty much any Dolphins fan in the area can tell you that. Great food, great service, every game is televised. It's like a United Nations of football; virtually every team has some fans there. The downside is you'd better get there early, because it gets packed quickly on Sundays. This is, more often than not, where you'll find me on Sundays.
The Elmwood, which is about half a block down the street, is another good one, and is generally considered a Dolphins bar. I've never actually watched a game there, but I've been there enough to know the food is good and the service is at least acceptable.
The Thirsty Turtle has two locations, one in Victor, one in Greece. They just opened up, and I'm not sure if they will be getting NFL Sunday Ticket or not. But they've got a whole bunch of TVs, lots of room and great food. Plus, a friend of mine manages one of them, so I'd be remiss not to give them a plug. :)
Buffalo is a bit less hospitable to Dolfans, and understandably so. I'm partial to Buffalo Wild Wings (3 locations, I think; I usually went to the one in W.Amherst on Niagara Falls Blvd) because it's pretty low key and the food is good. The service is pretty hit or miss. They've also got the NTN Network there, which features a game called QB1. You try to "call" the upcoming play, and if you're right, you get points. Incredibly good way to make a crummy game fun. They also have every game televised, but usually just two big screens, both of which will have the Bills.
I'd take a pass on Damon's in Williamsville. They have most, but not all, the games televised, and the Bills will usually take up a number of their TVs, though the Phins typically merit a big screen. Plus, the food is mediocre on their best day. I do have good memories of that place, though: that's the place where I watched Jay Fiedler's finest hour as a Dolphin, his 2 TDs rushing against the Raiders, including that ballsy 8 yard scramble for a TD in the final seconds.
By the way, at some point soon, I will be writing an article for the benefit of Dolphin fans visiting Buffalo for our annual @$$-whipping of the Bills at Ralph Wilson Stadium, so if you're coming out for the game, be on the lookout for that.