The single best way I've found to keep FPS up is an efficient layout of your fortress, where stockpiles are very close to their workshops and product drop off stockpiles. The bulk of my fortress is always on the same screen and not requiring scrolling, just build it up/down like an underground tower.
Other than that, the next best things have been:
Not having too many pets/animals
Minimal changes to water flows from however the map was originally
Small benefits from using traffic patterns (High, Low, Restricted) and painting places that the bulk of your dwarves should not be going to as restricted, like workshops.
Blocking off depleted mined out areas
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Other than that, it seems good performance is closely tied to the speed of an individual core/cpu. Dwarf Fortress seems to have either no or very little ability to utilize modern multi-core CPUs. Sadly, that's a problem that is getting more and more common. There are a lot of games out there that can be played with a scope so large and complex that it's literally impossible to play it because of the limitations of the programming.
For example, older PCs with a more powerful single core CPU (so long as their RAM and such isn't horribly slow) can outperform newer systems with multiple (but individually lesser) cores. A 3.2Ghz single CPU can do better than a modern quad core system with 4x 2Ghz cores or the like.