I've started to mod alot of fancy things, like tweaking tokens and changing prefstrings and specific internal organs, but with time it became obvious that the more you see something, the greater impact it will have while modded:
1) The most noticeable change in creatures is the variety of their attacks, because you directly see them every time you try to brawl them in adventure mode. A bit smaller change but still noticeable is a tweaking of bodyparts/organs, because you see this change every time you try to attack and succeed.
In case of creature attacks, long and creative descriptions (or just long, like "makes a high swing, hitting", "spits poison and bites", "makes a complex gesture and sends a blast of energy" etc.) make creatures more interesting and adds a nice flavor.
Too bad there's not a lot of "magical"/special ways to improve creature, just: firebreath, dragonfirebreath, webber for long range attacks and specialattacK_inject_extract, specialattack_suck_blood for close combat. Still with various damage types you can make "ice mages" which paralyze you with cold touches and poisonous vampiric creatures. Not a lot of possibilities, but with proper descriptions of attacks and creatures you have some field for creativity.
2) A bit lesser change but still noticeable is a change in entity weapons/armor, mostly weapons. If you give various types of damage and some side properties (like stick chance or crit. boost) to specific weapons, if gives you choice in what you're attacking with. In vanilla DF it's obvious that you don't have to pick a weapon in most cases, you just use the one you're more proficient with. If you make a creature like "treasure chest" which is immobile and drops a powerful random item on death, it makes those cave-divings and random wandering more interesting and makes you to change weapons from time to time. Too bad it's not the case with armor, because you have to make simple "metal chests", "ornate elven wooden chests
and special "dwarven rune chest" because dwarves are 1 size smaller than humans and elves are "narrow", which requires a special type of chest for every race (because the creature drops the armor with the same size and properties (i.e. stout, narrow) as it is. If you wonder about "random drop" I mentioned, there's a simple workaround: just make a lot of chests with various itemcorpses, but give them the same name. Thus you won't know what is the item inside when you encounter one.
3) There're various tweaks to entity namings (the words they use to describe things) and to entity values (slavery, theft etc. disposition) which do not matter a lot to gameplay (except for entity relations during the worldgen) but they add a nice flavor and allow you to further personalize entities and civilizations to your taste.
I don't remember a creature I haven't done, I mean there're always something new you can create, but I've made so many creature types it's hard to propose something new unless you're following some pre-defined setting. I've made exact versions of aberrations from Faerun, using my DnD books; I've made a complex humanoid body with different arteries, complete set of bones and even 32 teeth. But it's not fun when a single arrow pierces all your arteries in the body.
So the current engine is somewhat limiting. You may think that a creature with 2 hearts would be more durable than with 1, but in DF it's the opposite case. So you have to admit it when you make your creatures, as you told.
P.S. So the current way to make creatures "stronger" is to give them a bigger size (at least 1 bigger than dwarves, it makes the attack formula different) and give them some damblock or more arms so they have more shields to block.
Also NOPAIN and NOSTUN are really great tokens. Usually creatures pass out after 1 or 2 successful strikes in their vital body parts or after someone twists a spear in their tail a few times (this is how dragons die; thus i gave them NOPAIN and they became 10 times stronger).