I figured I could help out by explaining what and why these settings help out, plus add some of my own.
First off, the biggest thing that hurts my frame rate is pathfinding. Having animals run around, hurts the frame rate possibly more then having a big area. So, I usually cage all animals except a few wardogs, who I leash to ropes at keypoints in my fortress. This is because pathfinding (if I remember correctly), is done ever frame for every creature on the map. If animals are in cages, they don't have pathfinding on, thus it speeds the game up considerably.
Lowering the area is an obvious one, less things to keep in memory and process, then you have more time devoted to other things.
Temperature is a big one, Especially(!!!) if you have water or lava, as these are incredibly intensive on temperature. This is because everytime the temperature changes, I believe, it checks all the flow tiles (water, magma), and alot of the creatures for their maxinum or mininum resistances, and then deals accordingly (bursting in flames or freezing)
Having water or magma on the map, especially when you connect them to a channel and they start flowing, hurts frame rate, but this one isn't especially important. (I tend to have both a surface river and magma on my maps)
Back with the pathfinding thing, less dwarves, less pathfinding, less hurting your frame rate.
As for the whole frame rate when you go down Z-levels, I personally haven't saw this, mine seems to stabalize at around 80, regardless of whether I'm pictured on the surface, underground, or in the air.
Weather gives you an extra few FPS when turned off, and really, isn't needed at all. It makes your dwarves sadder, especially if they don't like rain or being outdoors, and so far, as far as I know, has no real disadvantages for turning it off. This probaly single-handedly jumped my framte rate by 20, with it off. No theories on why.
G_FPS, as was mentioned in an earlier post, deals with how many frames you 'see', versus how many frames are actually passing by. The standard human eye can only see about 26 frames a second, (not verified, could be off by a few), and most televisions have that frame rate in mind). 10 seems to be a bit too low for me, so I set it to 20. These seemed to help as well. This is probaly because, the less time it takes to 'render', the more time that it has to devote to pathfinding, and other things.
As for the first post, I believe Toady said he had fixed, or somewhat remedied the 'empty' or 'black' space bug.
Just for comparison purposes, the Pre-3D version ran at about 15-30FPS, which I thought was great. My current setup, runs at about 80-100 FPS, with a 6x6 area (usually around 40 Z levels), 10-15 dwarves, with a surface river and magma.
I hope this helps explain some, even if they are a bit obvious.
Kayla
Edit: Everything I said here is of my opinion, and may or may not be wrong, ignorant, or completely out of the ballpark. But experience tells me that what I said here is mostly true or as true as I can get without having the source code or Toady commenting.
[ December 19, 2007: Message edited by: Kayla ]