Well, turning off weather, any misters and removing flowing liquids could also help. Note that this doesn't affect evil weather, however (if you have reanimating embark, then necrosplosions in invisible caverns can eat into your FPS).
You might be able to function slightly better if you don't let DF use the main computer core, or even limit it to just 1.
I've read that retire/unretire has helped to salvage FPS lost from surface channeling in particular. It will also bring back any animal populations you killed off, however.
Dfhack does have fix/fat-dwarves, clean all, cleanowned....
Other modding, I've seen idea of removing rust, for instance, due counter effects. *quick check* Seems I get ~630 FPS with 84 dogs in freezing arena, each in 1x1 box (yay gui/liquids plugin), ~556 with 84 unskilled naked dwarves - but 450 when I give them all-around skills and military outfit. [43.03]
..And when I compared various morningstar materials yesterday, I got 90 FPS after 87 omni-grandmaster dwarves and 81 bronze colossi were chilling in their 2x1 individual boxes after the fighting stopped (I had the water running, though it by it's lonesome couldn't dent 1000 FPS).
(Not sure what it is with no creatures, but over 1000, which is what I've set my cap at.)
Might as well upload the save, though I'm not curious enough atm.