find ways to kill all the pets.
this makes things immediately go really fast again, to a point.
efficient suggestion - pit with atom smasher activated by dwarf walking down hall to drop pet. bridge goes up, pet lands in hole. dwarf walks away, bridge goes down.
more fun suggestion - a really deep hole, or a really tall tower. or a combination of both. bits of kitten bounce multiple z levels and can go a long way. careful of miasma.
also, any large scale projects which move water/magma around kill fps dead. especially waterfalls of any kind. its fun but in a big fort it sucks.
seal any unused exploratory mining tunnels and stuff. im pretty sure just a locked door cuts areas out of being investigated by the pathfinding AI.
turning off temperature and weather can help.
a very small starting area helps a lot. smaller the better. on an old computer consider the nanofortress tool for a 1 by 1 fort. you can also set a population cap in the init files to limit the total number of dwarves you can get.
bottom line - dwarf fort is not that well optimised, and inevitably for me all my forts reach a point where things get so big and there are so many things running around that even my fairly respecable computer cannot deliver the silky smooth speed it did right after the initial embark. tis the price we pay for having only one guy doing all the work, who dedicates most of his energy into giving us a constant stream of awesome new gameplay elements rather then carefuly streamlining every last bit of code.
you can search around for more tips on optimization on the forums, there are lots more things to do depending on your system.