I know people swear by this stuff called Nature's Miracle. Its enzyme-based and as far as I know, doesn't hurt anything synthetic. I mean, I could be wrong... but I have a relative who had 4 cats (3 of them were male) and everything at some point was marked. She would just spritz it with the Nature's Miracle, let it dry and it wouldn't stink anymore and I don't remember seeing any stains. She also has a little weenie dog that refused to be house broken... so... you can imagine how much of that stuff she went through. I think it's like $20 for a big bottle, not sure if they have smaller ones or not.
Personally, though, I haven't used it. And I agree with the other member about vinegar, too, it's an amazing cleaner. You can wash your clothes with it... but.. oh my gosh, it takes a while for that stank to get out. Bleh! Good luck!