Ashley,
Just add your geodatabase layers to ArcMap and group them. Then right-click on the group and select to Create Layer Package. If you do this in ArcMap 10, it puts both version 9.3 and 10 databases in the layer package. You can also use the Package Layer geoprocessing tool in Data Management Tools > Package toolset, and it will let you select what geodatabase versions to output.
After the layer package is created, just unpack and the database you want will be in the v93 folder. Maybe there is a better method, but this worked for me!
-Jane