Depending on the Continuity you follow, he actually has married both.
In the mainstream comics he is currently married to Lois Lane. This works well because in this way, it is Clark Kent that is married to Lois Lane. Two reporters that work at the same Newspaper married, which does not arouse a lot of suspicion.
In the possible future Kingdom Come, Lois was killed, and after some time, Superman finally marries Wonder Woman. In this case, he is no longer using the secret Identity of Clark Kent, and so it is 2 superheroes that are married.
So, I guess really it goes back to the age old debate: who is Superman? Is he Clark or Superman? If he is Clark and Superman is the façade he puts on for saving people, then by the above he should be married to Lois Lane as he will spend most of his life as Clark and should he have children, this will allow them to grow up and meet the Kents.
If he is Superman and Clark is the façade he puts on for a disguise, then he should marry Wonder Woman as he is primarily a Superhero and marrying another Superhero keeps his wife safe. Now, if we go by the fact the Wonder Woman now as the Secret Identity Agent Diana Prince, it is a little trickier because a Reporter and a Secret Agent seen together may arouse some suspicions.
I guess my overall opinion is that the stories work better having Superman be Clark Kent as the real identity, and being married to Lois Lane in the mainstream continuity leaving Wonder Woman to have her own universe.
Now, this does put together one big setup though. The events of both Kingdom Come and Infinite Crisis have shown this, what would Superman, who may be immortal and live forever or at least longer than a mortal, do when his mortal bride’s health eventually fails and she passes away?
If he were married to a woman like Wonder Woman, she is going to live roughly the same amount of time as he.
The other debate was brought up by Kingdom Come, how would they raise their children to have good human morals, both being of different worlds? In Kingdom Come they have Batman, but would they have anyone in the Mainstream Universe?
Could Superman and Lois Lane have children? If they do have children, could Lois die like the proposed Armageddon 2001 storyline from the old Adventures of Superman Annual #3?
DC Comics Fan