The following will help your FPS, or at least have been rumored to do so by the community in general. You're probably aware of most of them, but it might help someone:
Pocket World Gen
Shorter History Gen
Population Cap (I find 60 dwarves is a comfortable amount)
Minimal liquid flow (Dam rivers, keep still water at an even depth)
Minimal magma flow (Worse than water due to temperature calculations when it moves)
Machinery, particularly pump stacks. Usually goes hand in hand with moving lots of liquids.
Clean contaminants from your dwarves and walls (Make a bath, or use DFhack/DFclean)
Atom smash useless items
Shallow worlds and reduced cavern layers (Change in advanced world-gen). Or avoid discovering caverns at all.
Remove unused or excessive stockpiles
Don't use clothing outside of what dwarves bring in with them.
Don't designate excessively large things at once, like channeling out a entire z-level.
Fortress Design Efficiency
-Use ramps over stairs
-Build vertically instead of horizontally
-Use 3 tile corridors for high traffic areas, 1 tile for areas rarely used.
-Don't put one single tile chokepoint/doors for a high traffic areas, for example a meeting hall.
-Keep related buildings near each other and their related stockpiles; such as Kitchens/Butchers/Tanners or Carpenters/Wood Furnace/Forge
-Close off the outdoors when it's not needed with bridges, locked doors, etc, so it's not taken into account in path finding calculations.
Lower Baby cap (Mothers with 10 children following them around permanently tend to clog traffic)
Trade in low volumes of goods, such as one masterpiece roast instead of 30 stone crafts.
3x3 or 2x2 Embarks with minimal elevation changes
For building projects, turn off invasions.
Turn off weather
Turn off temperature