FPS is pretty intense stuff. I know I did a ton of reading on it when I was playing on my older and slower computer. The general KISS rule of thumb applies. Sealing off the caverns/outside/unused areas and destroying/forbidding/properly organizing items can do wonders for FPS. The goal is to clean up pathfinding as much as possible. Making point "A" a direct path to point "B" and try to limit alternate routes, columns, paths, exits, etc. From what I understand, it would be fine if every tile were passable, where every tile was an up/down stair, but that is generally not the case with fort design.
The best way I know of to deal with low FPS is to kill off a large portion of your population to prevent them from running worthless pathfinding calculations. Pasturing pets, livestock, and burrowing helpless cheesemakers under an atom smasher is a quick fix, but you can do some other more tedious things. I'm tempted to create a thread all about low fps fort designs and see what people come up with. I'm sure there are some ingenious designs out there that are beyond my comprehension.
Also.. avoid playing with liquids as much as possible >.>. *Sigh*
FPS is always a sad topic for me as it is like reading a list of things you "can't do" when dwarf fortress is all about removing limitations. My biggest recommendation is don't let FPS govern what you can and can't do. Just do stuff and try to be as patient as possible when the FPS begins to drop. It can be frustrating at times... but so can moody dwarves... the end products are worth it.
If FPS is still an issue, you can try the
Modest Accelerated Mod. I switch between using it and vanilla.