I made a massive improvement on my game speed by building a multi leveled fortress. Each level is small enough no scrolling is needed. Previously my floors were too big. So instead of expanding outwards much, go up/down. Additionally:
Things that seemed to have helped me quite a bit:
Walling off pointless areas.
Limiting/cutting access to large outdoor and cave areas.
2 or 3 wide hallways. This helps dwarves travel smoothly and lowers pet fighting - they seem MUCH more likely to fight each other if they are forced to occupy the same square.
Keep material relevant stockpiles very close to workshops that use that resource. Also significantly improves production response time and build efficiency.
Heavy use of traffic designations to make workshops, large stone stockpiles, and other low traffic areas less desirable for normal fortress traversing.
I use the Lazy Newb Pack launcher and I set the game at 100 Calculation FPS cap and 30 Graphical FPS cap. You can do this by editing the init.ini as well. My print mode is VBO, seems to work good on my card. I also use Soundsense (which is awesome) and the Ironhand graphic set. I have an Intel Core2Duo @ 2.93Ghz each core, and 4GB of gaming RAM that is about two years old. Windows 7. My graphics card is an MSI TwinFrozr 1G OC which is basically a faster NVIDIA GeForce GTS 250 with 1GB of memory. I haven't change any other things about the game like the temperature and weather, that's all stock.
I have the FPS counter displaying in game and it shows two numbers. I believe the first number is the calculation speed (how quickly everything moves and such) and the second is frames per second, which is just graphics. My current Fortress is about 5 years old, 143 Dwarves, around 220 pets. I have 2 waterfalls that go about 3 or 4 z-levels. One natural, one artificial. I use them for mist generators, two from the natural waterfall and one from the artificial one. But my game typically holds around 62-73 calculations and 29-30 FPS, which is capped at 30 anyway so it's basically unchanged. My previous less efficiently designed fortress had roughly the same Dwarf/Pet population, fortress age, and map complexity. When I decided to give up on it and it ran much, much worse. I've yet to ever utilize these atom smashers I hear about though, so maybe I could get even more with that but so far it's a nice improvement as that still feels like a reasonable steady speed. So it seems to me efficient design is the single best thing you can do besides having a good computer. Followed by finding which print mode works best for you.
You could try lowering the population cap, but if you do look into what you need for nobles and other things that advance your fortress as it seems many are governed by your population.