The water is not supposed to have a smell. If it does, there is something growing in it that's not supposed to be in it. Typically it's a type of fungus that's growing in it when it has a bad odor.

Mine never smells, but I think georgeiii's probably has a rather distinct odor.
~Ken~

Actually there's no smell because rot is a fuction of ph. Without ph worries the water is as pure as it went in. In fact if there's a smell it means something is unplugged. Once the air is turned back on the smell is gone. There's pictures at Photobucket/ChristianWarlock.

Bubbling (enough) air in your water in most cases will definitely reduce the chances or amount of fungi/bacteria/pathogens that can grow in your nutrient solution with the increased dissolved oxygen levels. But it's not a cure all, it will just suppress it from getting a strong foothold and growing uncontrolled. Root rot (caused by fungi/bacteria/pathogens) can grow in a wide range of pH (if not the entire range). But changing pH to a range that will kill fungi/bacteria and pathogens (if possible) will kill your plants as well. If pathogens couldn't survive in a pH range plants grow in, they never would have evolved to attack plants in the first place.

More important for the growth of these things is water temperature and light. Also keeping dead organic mater out of your nutrient solution will reduce the chances of your reservoir becoming infected by pathogenic organisms in the first place. Dead organic mater often has pathogenic fungi spores and bacteria attached. Even if it dosen't, it becomes food for them.