So, initially, I was trying to reproduce the look of GTA5's particles, so I tried baking out fluid simulations from Maya. The sim on the right was solved in 2d and was pretty quick to solve and render. The one in the middle was solved in 3d and was really really slow to work with. These two both have nice subtle animation, but they took forever to set up and to bake. The one on the right is generated completely from turbulent noise effects and masks in After Effects. I felt a lot more control here, and it was much faster to make (I'm very comfortable in AE, though, so your milage may vary).
These two effects were both hand made without a sim. The one on the left was made using the same kinds of noise effects as in the smoke effect above. The one on the right was animated as traditional frame-by-frame 2d animation in Flash and then modified in After Effects to add detail. I have a tutorial for how to do this on my Youtube channel, but suffice to say, it gives you a lot more control over the final look of the effect. That said, this technique doesn't scale well to effects longer than 32 frames long (or 64 if you're really patient). Because it relies on hand-drawn animation rather than tweens, as you double the length of the animation, you double not only the cost of keeping all the sprites for the animation in memory during the game, but also, you linearly increase the amount of work to make the effect in the first place, which is a problem that tweens don't have.
Anyway, feel free to ask questions if you have any. I have many many more flipbooks than these, but the ones here are fairly representative of the various ways I've tried to solve fire and smoke systems.