MySQL has a "nice" feature where all varchar searches are case-insensitive. I have a column which is a Base64 encoded key which I want to store as a String but need to perform case-insensitive searches on. In mysql you can create a column as "varchar(X) binary" and MySQL will perform all queries on that column as case-sensitive.

The problem is that we are using two different types of databases: mysql in development and DB2 for production so any solution needs to be portable. I can use a sql-type attribute of "varchar(X) binary" but that won't work on DB2 (at least I assume it won't work?). Ideas?

You are using SchemaExport I suppose? You could create your own extension of MySQLDialect and override the registered column type for varchar (look at the mysldialect). Anyways, using SchemaExport on Production Databases is questionable at best.