It sounds like superman should just impregnate his cousin. The risk of expressing genetic degradation is quite small, and certainly less of a problem than the scenario described above, ie, supersperm hunting down every ovum in metropolis.
(Depending on the recessive genes he shares with Supergirl, of course. Possibly a severely retarded kryptonian would be quite a problem.)
One has to assume that he spent puberty concientiously ejaculating into the sun in order to avert just that sort of disaster.
He would definitely have to be outside while punching his way into heaven. After the first hole blown through the ceiling, it would be hard enough to explain to his parents. As far as I can tell, sperm responds to chemical cues and tends to speed up dramatically when it catches the right signal. If he were to bust into the sun, it would dramatically decrease the potential boom in population. I learned that sperm really likes the smell of L-tryptophan...at least earthly sperm does. I would hope that the chemical signature was blocked by the composition of his semen to prevent the propagation of millions microscopic wormholes and sonic booms in the sperm's desperate attempt to rush a fertile egg.
He's got the option of Supergirl and Powergirl, they're both his cousins, though Powergirl is from a parallel universe. It's been shown that genetic degredation between cousins is only slightly more serious than two essentially unrelated people. However, there's a very small pool of gene variety, so that would only be safe for the generation created by Superman and his cousins. Any further than that and weird stuff happens, assuming Kryptonian DNA acts anything like good ol' human DNA.
Really, the only person who could possibly impregnate either of those Kryptonian women is Superman. For one, the muscles in their vaginas would either completely prevent penetration or, if the guy was lucky (and this is the worst kind of lucky ever), his manhood would be destroyed. Crushed beyond all recognition. If he survived unscathed and somehow his sperm made it (by complete failure of the Kryptonian immune system), it would have no way to get through the cellular wall of the egg. Now, if some method of fertilization was devised (possibly by weakening the eggs with kryptonite), in vitro could work. Gold kryptonite is an option, as it removes a Kryptonian's powers permanently while leaving their genes intact. However, that means leaving the current generation essentially powerless. But, the kryptonite could be used on either the eggs or sperm, which leaves it to be seen if the kryptonian genes are recessive or dominant. If they're recessive, normal human baby. Dominant means the need for a super-uterus. Imagine a fetus with X-ray vision; enough of that could sterilize a human mother. Now imagine heat-vision. Now, as I said before, a super fetus punching its way out into the open air. It's not a pretty sight.
I expect it's something to do with cheap rolex watches enlarging his penis while he makes $400,000 an hour working from home.