You can't eliminate the smell, but there are lots of things you can do to keep it from getting out of control.

- good bedding (Equine Fresh seems to get the best reviews over all, I use it but haven't used others so I can't really compare)
- change bedding often
- don't overcrowd
- adequate ventilation
- vanilla in water

Another tip is to NOT totally clean the enclosures. I dump out the bedding, but then just add new bedding, not washing the tub at all (unless I'm putting different mice back in). This is because they mark their territory, and if they can't smell their markings, they'll go around and make a bunch of new ones, instantly raising the stink level even though you just cleaned the cage.

Also, the males are the stinkier ones. I've noticed some males are quite a bit stinkier than others, so you could just eliminate the stinkiest boys. I've been toying around with the idea of not taking holdbacks from the stinky boys' colonies to selectively breed for less stinky mice. I'll probably get around to it eventually, but right now a higher priority is to establish a really good bloodline for raising lots of big healthy babies.