Hi Katherine, we went through a selection process for the database back end. Our situation is a bit unique, because we have an Oracle site license, so buying a separate license of SQL Server just for our web database didn't make much sense, although we did look into pricing.
We ultimately chose to use MySQL for our mojoPortal production database. SQL Server Express 2008 R2 has expanded the maximum disk space available to the database from 4 GB to 10 GB (which is WAY more than we needed), but it's also limited to 1 CPU, and 1 GB of RAM, and we didn't want to be constrained in that way.
I don't think there are any cons to mojoPortal running on MySQL. It's working great for us, and Joe has said that he uses it as well. If you go with MySQL, I'd also recommend you get HeidiSQL for database management. It's an excellent Windows open source solution.