I say give them hardened bodyarmor and the ability to spray magma from their palms (which is possible). Also, increase the toughness to about... say... 20x. Lasers might be awesome too (wouldn't be technically "lasers" but it'd get the job done).
I'm joking about all of this, but now I really want to mod again.
Maybe a chicken. I'll keep the chicken normal sized and, in the theme of Crysis, create a "nanochicken". It will "wear" a "nanosuit" that will allow it to heal incredibly fast - it will have such strength that it can fling dwarves against walls with ease - it will have such speed that it can hunt even the fastest and most agile of dwarves as if they were no faster than slugs.
But that's not quite a civ. I'll still probably make it.
Does it have to be humanoid? The last (and first, really, unless you count the manamaids, which were a joint effort) civ I made were the scythods, from scratch. I'd post the raws (I'm eager for opinions) but I think Mr Frog might not like that (he's designing a mod with the Scythods as one of the main civs). Their "feet" are four foot spikes, good for stabbing through victims. The lower arms end with claws, and the upper arms are basically rock-hard scythes that can sever limbs, ending in a "suction grasper" that can pick things up by suction, yet close to a sharp point capable of piercing enemies. Once the tip of the arm is inside an enemy's body cavity, it can reopen, locking on to the inside of the unlucky victim. Its teeth are on three dentaries (like snake jaws), which are attached to the top of the limbstalk, protecting the mouth. It has no head, and no eyes, as it "sees" via sonic vibrations. It's about as alien as it gets, and capable of taking on ten dwarves at once, unarmed. A single one can slay a dragon (provided it dodges the fire).
I really like Loud Whisper's idea about the sky whales and dwarven avatars, though honestly that's a bit too basic for my tastes (though I loudly applaud their badassery). HugoLuman has a mod I've been meaning to try out - Daleks. As I'm somewhat of a Doctor Who fan, I'd very like to see my dwarves break to pieces on them. Weeping Angels sadly aren't possible, but it would be nice - a race invincible to anything but traps (probably obsidian generators and cave-ins only).
Ah, but I'm digressing... and horribly so.
Use the wiki. The magmawiki may not know all, but it knows more than enough. I've been modding less than a month, and I'm greatly enjoying it (despite getting my many folders mixed up
lol ). Soak up all the wiki has to offer. You'll be modding pro in no time at all - it's not that hard, really. But then again, I'm a programmer, so, I don't know. (I still don't think you'll have trouble. lol)