I have found one very simple way to easily change the frame rate in my fort. Doors! Sealed ones.
I realized that whenever I started large scale mining operations, my game would soon begin to slow down very noticibly. I had huge grids of tunnels sprawling out beneath my fortress. Like many I blamed all those little rocks, but that wasn't it. Quite simply, it was all the extra squares I was adding to the path finding grid. Different patterns of space have different costs, but rather than worrying so much about arcane pathing patterns, you should be trying to do away with spaces altogether when you aren't using them.
Luckily, DF is very good at compartmentalizing its path finding spaces into separate 'regions' whenever you close off a space with a sealed door or wall. (not sure about un-traversable open space) In fact, you can easily see this by putting a door in some critical spot that cuts off one large chunk from the rest of the map. When you seal this door, you will often actually see the game hitch for a second - I believe this is the path finding system running through the entire space, determining if you just segregated the pathing space into multiple regions.
The moment you do this long range pathing costs for entities in either of the newly created regions drops, and you should see a frame rate increase.
So simply put, don't dig endless warrens throughout the underground and leave them open. When you are done mining in a section, seal it off with walls or doors. When you break into a cavern, wall it off, or create a segregated section to 'live' in the same way you usually do on the surface, with sealed doors closing it off. As long as you do this and keep the main body of your fortress a reasonable size, you will be able to manage your frame rates.
As a note, I think this is why breaching the FHS reportedly massacres path finding so badly. Not only are there many smurfs, but they are generally flying/building-destroying smurfs who impolitely ignore most path restrictions and calculate their way using the ENTIRE path grid regardless of how it is broken up (including all those empty air tiles in the caverns...)