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[nop]

some science here:
I tried to find out of what is the most important source of FPS death. Sure, dffortresswiki says about potential sources, but not about the impact. So, I conducted several hundreds of experiments with fresh worlds with different histories and sizes, with multiple embarking locations, varying temperature on\off, hills, rivers, oceans, different pets (136 kittens, 136 ducks, none, etc). FPS cap was set to 500, 'startdwarf' dfhack script was used to alter the number of dwarves on embarking. The goal was to find out of what is happening right after embarking, because FPS of the developed fortress will be even less.

These have the major impact on FPS: number of dwarves, ocean, temperature, the number of pets (such as kittens), neutral birds (completely kill FPS from time to time).
Does not seem to have effect / very minor effect: world size, history, size of the starting location (4x4, 3x3, 2x2, 1x1 all give the same FPS unless you have kittens), trees, plants, hills, streams, breaching magma sea and caverns

[Insert_Gnome_Here]

I think one of the big sources is pathing. 
I've never tested it scientifically, but pasturing all my animals somewhere with a door tends to lessen the effect on FPS.

[TheEqualsE]

I can back you up on things I've seen in earlier versions, and I don't think it's changed that much.  I've seen a flock of birds arrive on the screen causing a huge fps crash.  I've seen 20 crundles step onto the map in the caverns causing a noticeable drop.  Waterfalls that are short and direct don't cause much fps loss so streams should be even less than that.  Breaking into caves really shouldn't change fps that much if your dwarves don't have a reason to be in them.  For instance, in my fort I recently locked all the entrances to the caves.  Normally I have a few people gathering webs, now suddenly they couldn't.  For blocking off all the caves the fort got MAYBE 1 fps back, maybe not even that.  It's hard to say exactly.

At the start of the game I wouldn't expect there to be a lot of big, old trees around.  Get enough trees on a big embark and I think eventually they would become a factor.  Not as big as the number of dwarves, but responsible for some FPS loss.  I don't think they ever stop growing either, so even a place with fully grown trees will constantly try to grow new ones any way.

[Bapdorf]

How sure are you that the size of the starting embark has little effect?
It may be the case, but that really feels like something that would be major, and seems like it has had an effect to me; However it is possible that these arise not out of the size itself directly I guess, but instead secondarily from the increased flora, fauna and pathing. I'm certain it must do something, because I exceed 400fps on a 1x1, but stutter all over the place between 80-120 fps (on start, with 7 dwarves and no pets) on a 10x10. Cause would be nice?

[Ggobs]

I also notice having a bunch of ore laying around hurts fps. Also products that aren't in stockpiles.

[Halnoth]

I also notice having a bunch of ore laying around hurts fps. Also products that aren't in stockpiles.

That probably has to do with the jobs generated to take said items to their stockpiles. The jobs would cause an increase in pathing. Especially ore which is probably not located right in the middle of your main walkways.

[TheEqualsE]

How sure are you that the size of the starting embark has little effect?
...

I've experimented with this a little.  From what I've seen a larger embark has the same impact as a certain number of dwarves.  For instance I can do 200 some guys on a 3 by 3 or 3 by 4 embark and still have pretty fair fps.  If I was going to do a 5 by 5 it would "cost" 10 or probably 20 dwarves to get the same fps.  I would expect a 10 by 10 to come at a more severe cost.  People with nicer computers could add more dwarves or a larger embark to get the same results.

I feel it's partly the trees and plants constantly trying to spread, because it also depends on what's in those tiles.  a badlands with no trees whatsoever isn't going to hurt fps as much as a forest, which wouldn't hurt as much as a mature forest with a ridiculous amount of trees in it.  The cave levels matter too - caves with no water produce no mushrooms.  Any fort that has one of those is going to run a little faster.

I experimented with playing larger embarks because cave layers with no water are not that uncommon.  I got lucky a couple of times in a row.  It's great when it works, but it backfires if you try it and it didn't happen.  If you like playing with a bigger fort, which I do.