The following things are known lag producers:
Any necessity to climb due to being otherwise cut off. (I had a miner trap himself in a silly channeling path choice, and it immediately dropped my FPS from what was 100 FPS even when I got double as many dwarves as I had then, down to 20 or so. This is a brutal drop to FPS that is notable with even a single pather.)
Large numbers of existing items or creatures, dead or alive. Dead creatures still cause lag. (They are tested every frame for status, even after their corpse is atom-smashed, and can never be raised by a necromancer.) Consuming or atom-smashing items reclaims most of the FPS, but not all of it. Quantum stockpiling also reclaims a portion of FPS.
Items with detailed information, like engraved floors or decorated objects cause more lag than boulders.
See Operation FPS Bomb for more information.
Multi-tile trees. Have you considered a nice desert, savanna, or glacier?
Moving water or magma. Just try to drain the ocean into the caverns and see what happens to your FPS. This makes dwarven perpetual motion devices serious FPS drains.
Opening or closing doors by lever, or movement of drawbridges (such as atom-smashers). These force a pathing connectivity check that tests your whole embark.
Wide open spaces massively snarl pathfinding. Wall off spaces you don't need anymore to prevent pathfinding through them. Better yet, just mine less of your embark, and play on a smaller embark to start with.
Not using traffic designations as they were intended (especially not using them at all) causes more pathfinding problems. If you aren't going to use traffic designations to paint major arteries as high traffic and paint the edge tiles of workshops as low-traffic or restricted, you should set normal traffic to 1 to cut your pathfinding time significantly.
Using a single central up/down stairs pipe. The game is optimized to pathfind over ramps. Central stairways also tend to flood hallways with dead-end paths.
Leaving all the performance init options on. Turn off temperature checks or weather to make the game go a little faster.
A few other things I probably forgot...