In case Hooberus doesn't make it by today:
From: http://www.answersingenesis.org/articles/am/v2/n2/caring-for-the-animals
(This is only an excerpt, I encourage you to read the entire page. VERY entertaining!)
What Did Noah and His Family Do with the Animal Waste?
As much as 12 U.S. tons (11 m. tons) of animal waste may have been produced daily. The key to keeping the enclosures clean was to avoid the need for Noah and his family to do the work. The right systems could also prevent the need to change animal bedding. Noah could have accomplished this in several ways. One possibility would be to allow the waste to accumulate below the animals, much as we see in modern pet shops. In this regard, there could have been slatted floors, and animals could have trampled their waste into the pits below. Small animals, such as birds, could have multiple levels in their enclosures, and waste could have simply accumulated at the bottom of each.
The danger of toxic or explosive manure gases, such as methane, would be alleviated by the constant movement of the Ark, which would have allowed manure gases to be constantly released. Secondly, methane, which is half the density of air, would quickly find its way out of a small opening such as a window. There is no reason to believe that the levels of these gases within the Ark would have approached hazardous levels.
Alternatively, sloped floors would have allowed the waste to flow into large central gutters. Noah’s family could have then dumped this overboard without an excessive expenditure of manpower.
The problem of manure odor may, at first thought, seem insurmountable. But we must remember that, throughout most of human history, humans lived together with their farm animals. Barns, separate from human living quarters, are a relatively recent development.
Dave