Karsten is right. You may be able to kill or mask the mildew on the top of the carpet but if it's bad enough to notice in the first place, it's almost certain that the mildew will be growing underneath the carpet and in the padding if you have any. If it gets that deep, you'll never be able to get rid of it.

Best bet probably would be to cover the basement with something water proof like tile, vinyl, or paint, and use rugs to make it more 'homey'. If you want to get really fancy, I've seen tile and vinyl that has the look of wood.