My current fort is a 4x4 embark, with 220 dwarves, and I am maintaining 140-160 fps after 17 years (I have a nice new i5 machine slightly so these results are not typical). I have tried several things many things to try to keep my fps up, I will go ahead and list as many as I can remember as well as my impressions. I will include my thoughts on how I believe each part impacts my FPS in (), but most of this is wild guessing on my part.
All of my non-critical dwarves are in the military, and set to no schedule. I have each squad set to its own small barracks so idle dwarves train in small rooms rather than gather together. This seems to be my biggest FPS saver. I am not sure why, but having a large number of idle dwarves seems to be my biggest FPS killer. I once had 40 idle dwarves at 120 FPS, I told them to dump all the damaged shirts and pants (probably 500 items), and my FPS went up to 170. This surprised me a lot, because I basically had 40 dwarves pathfinding halfway across my fort and down 130 z-levels for several hundred items. I expected that such a huge number of pathfinding jobs over such a large distance would kills FPS. Instead my FPS climbed quickly, and topped out before many of the items were destroyed. It is possible that the pathfinder is able to reuse paths, so having a large number of dwarves pathing to the same spot may actually be very less intensive than letting the stupid little guys wander to wherever they want to go.
I kill every animal I can, they seem to work like idle dwarves. I have no meeting halls, I think having all my dwarves in small groups in small rooms is much better for FPS than having them all stand around in a big room. Every dwarf has his own small room, I just build them, designate them as rooms and let the dwarves claim them. This does the same thing as the training rooms, keeps dwarves isolated in small rooms. I use large custom stockpiles that are set to store almost everything, I thought this would hurt FPS but I keep adding stockpiles and FPS stays high. I try to keep all my old clothes purged, but it is very management intensive to dump all my xSocksx. Dumping the items does seem to help fps a bit, but not a huge increase. I use a 3x3 central staircase, I have tried ramps, didn't seem to help.
I also try to keep most of my fort on a single z-level, the only z-levels that I use for something not on my main level are out of laziness rather than good design (or mining for ore). I usually use dfhack to clean my map every year, but that doesn't seem to impact FPS, it just makes my fort look cleaner. I am not using a dwarven bathtub. I have sealed off the caverns. I frequently claim my outside map of all goblinite, I also dump all goblin corpses into magma rather than letting them sit in the sun. Temperature is turned off.