Out of other parameters, temperature and weather have substantial effects on FPS and can be turned off unless you work with fire, magma, ice, evil biomes or murky pools.
As far as embark location goes, a forest can have a large impact, especially as season changes and all new growths pop up. Furthermore, since lot of calculations are per tile, doing smaller embarks and generating thinner worlds are helpful.
When designing a fortress, clear non-interrupted paths are preferable. Digging may be hardly avoidable, but a door linked to a repeater can cost a bit, though bridges have their own special place in hell (even a retracting bridge on flat ground in fresh embark linked to repeat lever will visibly stagger the game every time it toggles). Getting back towards the original thread topic, this also includes the changing squares of pathable and unpathable water near, say, where river flows off the map (beyond the cost of the water flow calculation itself), classic dwarven water reactor or the pump mist generator it is powering, should the pump ring be rotating 4+ water. (Mist, smoke and miasma have lesser effects that are however much easily caused in mass.)
Oh, and in actions every job seeks materials/dwarves as well, so large stockpiles/engraving areas can cost a bit.