If you sell stock in a company under a Roth IRA and that money goes into a money market account within the Roth IRA, how is the sale treated if it results in a loss?

All trades within any type of IRA is ignored, whether it results in a gain or a loss.

To add the BPicker response: because none of the transactions have an impact on your tax return in the year you trade, your recordkeeping is simplified. You keep track to know how well you are doing, not for IRS reporting. Wouldn't that be nice for taxable accounts!