Okay, taking my last post and running with it...
Koopas, like all reptiles in the Super Mario Universe, are a hermaphroditic species. There are no "female" or "male" Koopas; the concept of gender was only recently introduced to them through cultural exchange with the Mushroom Kingdom. Koopas that have visible gender identifiers are just imitating humans.
Koopas don't mate for life, which is why Bowser's never been seen with a mate. Instead, he's had several partners who sired his children like so:
1st mate: Ludwig
2nd mate: Roy and Morton
3rd mate: Wendy
4th mate: Iggy and Lemmy
5th mate: Larry
As for his last child, Junior, Bowser decided he wants an heir to mold perfectly in his own image, so he somehow impregnated himself, possibly with the aid of his Magikoopas. This is why Junior looks almost exactly like Bowser did as a child: he's basically a clone.
Why does Bowser keep abducting Princess Peach? Not because he's physically attracted her. It's purely symbolic in that he's holding the heir to the Mushroom Kingdom hostage. His occasional attempts to force her to marry him aren't for the sake of procreation but just to consolidate his power over both nations.
Why does Junior occasionally refer to Peach as his mommy? Because he's a dumb kid who doesn't know where hatchlings come from.
So there ya go. Irrefutable proof that I need to get my brain checked.