Utility wise I use Dwarf Therapist (makes the game playable*) and DFHack (but only the "get rid of FPS killing blood/fluids" part).
Mod wise I use Fortress Defense II (which, IMO, makes the game 100% more fun by virtue of making it 1000% more dangerous. Having to potentially wait years just to see a serious siege (by which point you should be completely prepared to handle it) is far too easy for my taste.. My most recent (sadly dead..) fort has had 'vile forces of darkness' arrive at least five or six times (often at the same time, so double the size siege) and its like three years old. I sometimes play around with Kobald Kamp too.. And mixing that with FDII.. Wow.. Epic..
-MB
*I'm sorry but I agree with the poster that commented that a flaw in DF is its lack of in-game UI to handle the complexity it offers. Don't get me wrong I love the complexity of DF, and I also know its 'alpha' and that someday toady will work on the UI, but the fact taht the majority of fans feel its not only helpful, but necessary to have a third party program just to play the game to me is a big flaw outshined only by, perhaps, FPS issues (as "FPS death" should not really exist at the rate it does).
I get it, they are going to hopefully be fixed one day, but a flaw is a flaw, if it wasn't it wouldn't need fixing.