We recently noticed water coming up from a crack in the ceramic tile of our bathroom floor. The water coming up from the crack in the tile has an odor and the cracked tile is close to our vanity/sink area. We also noticed that the base board and bottom of the bathroom cabinet/vanity looked water damaged and warped and we pulled it back to discover that the wood is rotting out. We don't see any visible leaks in the pipes...but have noticed another leaking area on the outside of our house on the same wall as our bathroom near the foundation. We have owned the home for 2 years...it is about 20 years old and I do think there has been some settling in the house. Where should we begin in figuring out where the leak is coming from?

If you are on a slab, you may have a leak on one of the water pipes under it. This is not an uncommon occurance.
Check to see that all the faucets and fixtures are not dripping water and then note the water meter reading. Go out for a while and then when you come back check the meter again. If it has moved you have a water leak.

Your homeonwers insurance should cover this repair, which in many cases can top 20 grand when all is said and done.

If the ceramic tile was added after the plumbing was laid, then pull your toilet and check the seal underneath. The additional height of the floor can create a gap that a single wax ring cannot seal, allowing wastewater to seep under the tiles. It is nasty stuff and other nasty things love to grow in it. A quick and common fix is to stack two wax rings on top of each other and reseat the throne but there are also adjustable seals sold for just this problem.

Good luck!