I'd like to start by saying, not all of these are original. Some of these may very well be, and probably are, already up in other threads. However, I figure so long as one idea is original then its fine. I only checked one of my ideas, and since that wasn't up I could follow the above logic fine.
Dwarven Sexuality
The thought first hit me when it came up in my Nation States game which I made after one of my forts. Why not have gay dwarves? And Lesbian and Bisexual for that matter. Add a bit of realism to the game. Hell, you could even add it as an optional crime for all those conservatives out there.
Crime and Punishment
Ever think that the punishments are too harsh? Or get pissed off at your nobles for getting the hammerdwarf to beat the shit out of a dwarf because of a mandate that wasn't followed? Well, why not be able to set what is a crime and what isn't yourself? And you may as well be able to set the punishment for certain crimes yourself too. Also, another thing that could be added to the crimes would be going into a restricted area, so that rather than making dwarves not WANT to go through that area, it makes them avoid it at all costs.
Low Quality Goods
Something thats been bugging me is that there are higher grade items, but no lower grade items. It makes no sense to me that the worst that a dabbling dwarf can make is what some competent dwarves normally make. So rather than having a standard item being the lowest possible quality, why not add worse quality items? Like a Flawed Toy Hammer or something?
Uses For Poison
On the startup menu there are poisons you can bring with you, but there seem to be no use for them. Why not make them part of traps? You could have a poison dart trap, so a terribly weak dart delivering a deadly poison would make for a decent trap. Or even add it as an option for an army dwarf to use on his weapon.
Stone Beds
This one I know has been mentioned before, but felt like it should be mentioned again. Dwarves are supposed to live INSIDE of mountains, meaning they should have no reliance on wood or other things one would find solely above ground. Rather than making wooden beds a necessity for a bedroom, they should be a luxury with stone beds being the norm.
Tree Growing
It takes a lot of time for trees to grow in areas where there are trees, so why not be able to grow trees like you do with other plants? They could still take awhile to grow, but it would make it less of a problem waiting for trees to grow.
Sandbox Mode
A lot of these sort of games have Sandbox Mode, where one can do pretty much as he pleases, edit the terrain, edit what you have and some such. This could be useful for those just starting the game, or those looking for a VERY specified fort location. This could be a sort of one shot fortress even. Though it would probably take a lot of work.
Forced Sparring
I've seen a few people having problems getting dwarves to spar, and I myself have had little luck with it, so how about adding a sparring location in a squad's menu? And add "Spar" to the list of options rather than just on and off duty. It'd make it easier to train dwarves, and would be a bit more realistic to be able to force them to spar then it is to just let them when they feel like it.
I had more that I thought up in Chem, but forgot on the bus ride home so this is all I've got.