There are some rules covering reproduction in D&D, but not in 3rd ed; however there are plenty of official indirect examples in 3rd.
Half-elf, half-orc, half-dragon, half-ogre, half-minotaur, half-dwarf (called a "Mul"), the sorcerer class itself, bloodline levels, the owlbear, the rohch, and so forth; there are many official examples of what happens when one has parents of disparate species, has a different sort of ancestor hanging in one's family tree, or falls afoul of meddling wizards or Dragons or Powers.
But have you heard of the orc-kobold? Or the pixie-storm giant? (The latter being Gygax's own creation, no less!) Probably not, unless you are a D&D grognard, or have a parent who is one.
Thoughts of new racial crossbreeds abounded during the 1st and 2nd edition eras, and the are even rules published about some, usually in Dragon magazine.
Here is a short list of some of the sources:
"Dragon's Bestiary: Magical Crossbreeds, The" Jonathan M. Richards 243(75) D&D2
"What Do You Get When You Cross..." John S. Olson 44(19) D&D1
Dragons "Crossing Dragons With Everything" Gregory W. Detwiler 170(19) D&D2
Half-dryad "Hooves and Green Hair" Bennet Marks 109(58) D&D1
Half-dwarf "Monstrous Side of the Dark Sun World, The" Brown & Connors 173(16) D&D2
Half-giants: DARK SUN "Monstrous Side of the Dark Sun World, The" Brown & Connors 173(13) D&D2
Half-ogre "Half-Ogre: Smiting Him Hip and Thigh, The" Gary Gygax 29(12) D&D1
Half-orcs: "Half + Half Isn't Always Full" Paul M. Crabaugh 44(20) D&D1
Variants "Half-orcs In a Variety of Styles" Roger Moore 44(17) D&D1
Half-satyr "Hooves and Green Hair" Bennet Marks 109(58) D&D1
And this is just a partial list.
Quite a few of these half races were also released in 3rd edition.
What suggestions are given typically use the Punnett square (from genetics and blood types) and also recommend giving children weaker and watered down versions of their parent's powers, probably only some of their powers, not to mention a shorter lifespan and possible sterility.
No super powered offspring to be found in these old suggestions.
While not 3.x material, perhaps this can provide some background and possible guidance, if one has the references handy.
Furthermore, even though polymorph affects type, unless the change is permanent, severed parts revert (if I recall correctly) which would include, ah, microscopic parts too, I do believe.
Thus, unless it's a permanent change, it shouldn't affect the reproductive process.