I would get advise from a professional.  Pet stores have cleaners but it sounds like you are beyond that.  Urine can penetrate deep well below the surface.  Replacing floor, cleaning the concrete, replacing baseborads, doors, might be the last resort.  It will be costly but the smell will be gone.  Seek advice from disaster cleanup professionals.  They probably fix lots of disasters.

 I suggest odoban.  You can buy it at home depot.  Its wonderful!!!

 Maybe email the Queen of Clean and see if you replies with an answer..

Thanks for your replies everyone! 

Who is the Queen of Clean?

I should have clarified that the smell is much more "old" and musty than specifically cat-pee.  I wonder if there is some rotting / wet wood somewhere.  I did have a clothes washer until very recently that leaked with each load I did...

I will try the black light trick to detect any possible pet spots, and try to be even more diligent about cleaning every single nook and cranny of the place as often as I can and airing out the house now that the weather's nice.  I hope this helps.  It's one of those smells I don't notice when I am in the house, only when I leave for a while and come back, but my boyfriend notices every time he comes in, and he HATES the smell.

 Again, if you have more suggestions, please keep them coming!

my mom has that and it is more damp crawlspace and lack of heat in the bedrooms etc.   there is that smell..

If it turns out that cat pee is the problem, we used some stuff called "kids and pets" (from Walmart) when Budders (the dog) was a puppy in house-training.This stuff is incredible.But if you find that the smell is comming from the flooring, I suggest you get the floors re-done (rip  out old carpet and replace, have hard-woods re-done) Have fun...this may be a good time to have you house done with your favorite colors, choices of floor coverings, etc!! .Congrats on buying a house with savings...I'm impressssed!!

Pet odors and kids spilled milk are especially nasty odors. The smell is caused by a bacteria/protein that actually eats through fabric and wood. You need something called "uric acid neutralizer" which you can find in vacuum supply stores and hardware stores that rent steam cleaners. Uric acid neutralizer is the active ingredient in all those expensive pet odor sprays. It will reduce the occasional fresh pet or milk accident out of your rug to the point the stench doesn't knock you over, but if your kitty peed there repeatedly (which they often do) or it sank down into the carpet pad and dried you'll probably need to rip out the rug. If it sank into the subfloor, especially if you have that cheap particleboard under your carpets, you'll have to rip out the top layer of subfloor, but if you have plywood or hardwood floors just scrub it down well, hit it with uric acid neutralizer, then once it dries spray it occasionally with plain old rubbing alcohol in a spray bottle to see if that kills the odor (the alcohol could damage the finish on your floors, but it's cheaper than replacing the entire floor). With both kids and pets always having oopsies, we replaced our carpets with hardwood floors and inexpensive area rugs that can just be dragged outside, hosed down, and left to dry in the sun.

Also, try a dehumidifier in that room for a while and see if that reduces the odor. It will help you decide whether it's pet odor or mold (or a combination). If mold is your problem, you're going to have to rip everything out (possibly including sheet rock), scrub the studs and subfloor down with a special mold killer/bleach solution (available at home improvement stores), let it dry thoroughly using a dehumidifier, repeat 2-3x, then redo the room. Mold is both nasty and toxic, causing allergies and asthma attacks. We had a leaky dishwasher hose leak down into a room in the finished basement below and we had to rip out everything down to the wall studs. Nasty stuff.