Travis West, Almost every house I buy to renovate stinks really bad and it's almost always pet odor. I've done a lot of research on mitigation and have tried several techniques. Your situation might be fairly simple to solve since you're sub-floor is concrete (wood sub-floors can be very difficult to get the smell out).
Before I go further..... I've come to realize that it's best to make the decision up front to be patient with the process because rushing through it could ruin your efforts to get rid of the smell. There's nothing more infuriating than new carpet that smells like dog/cat pee so be patient. It will likely take several days to solve the problem.
Here's what I would do...(assuming you have concrete subfloor):
1) Scrub the floor with a very strong cleaning agent like Simple Green or some other industrial strength cleaner. Put fans on it to help it dry and check it to see if the smell is gone. This works great if the offending smell is on the surface. If that didn't get rid of it....
2) Bacteria is what's causing the smell so you need something that will kill it. There's two ways to do that. a) Use an enzyme cleaner which seeks out and eats the bad bacteria, or b) Use a bacteria killer like bleach that kills everything living that it comes in contact with. Enzymes work very well and leave no unpleasant odor but they're very expensive so I would probably opt for the bleach technique first on your concrete floor. CAUTION: If you use a high concentration of bleach you will probably have to use a whole-face respirator that's rated for gas filtering. Bleach is dangerous so be careful. After the bleach solution dries, check again to see if the smell is gone......if not....
2-alternate) If you would rather not mess with the bleach, this would be the time to try the enzymes. Now that the floor is very clean, the enzymes should penetrate the floor with ease. Just follow the instructions on the bottle and you should get good results. The best place I found to buy it is at pet specialty stores like PetSmart. You might be able to find them at Walmart, Lowes, or Home Depot but I didn't have any luck with that.
3) If you've done steps 1 & 2 correctly, the smell should be nearly gone. To finish it off, you can coat the concrete with a high-density sealer like shellac. Odor molecules are smaller than paint molecules so don't waste your time and money using any kind of paint or primer because the smell will go right through it. My experience has been that this step always eliminates the rest of the smell.
That should take care of the problem you're working on but if you every have a house that's just generally smelly, I found that I can eliminate most "general" smells by using a high power ozone generator. The kind I'm talking about generates ozone at (lethal) levels high enough to kill everything living in the house (including the bacteria that's making the bad smell). This works great for vacant houses where there are no plants or animals living in the house. Ozone (O3) is very unstable and harmlessly turns into oxygen after a few minutes so there are no chemicals or other residue left when your finished. You have to use these machines with caution but, if done right, they work very well for eliminating almost any smell. Most of the large equipment rental companies carry these so it shouldn't be too difficult to put your hands on one. Make sure you follow the instructions carefully though.
Hope this helps. Good luck.