<p>I'm hoping to find out what tools folks use to synchronize data between databases. I'm looking for a JDBC solution that can be used as a command-line tool.</p>

<p>There used to be a tool called Sync4J that used the SyncML framework but this seems to have fallen by the wayside.</p>

I have heard that the Data Replication Service provided by Db4O is really good. It allows you to use Hibernate to back onto a RDBMS - I don't think it supports JDBC tho (
http://www.db4o.com/about/productinformation/drs/Default.aspx?AspxAutoDetectCookieSupport=1
)
There is an open source project called Daffodil, but I haven't investigated it at all. (
https://daffodilreplicator.dev.java.net/
)
The one I am currently considering using is called SymmetricDS (
http://symmetricds.sourceforge.net/
)
There are others, they each do it slightly differently. Some use triggers, some poll, some use intercepting JDBC drivers. You need to decide what technical limitations you are under to determine which one you really want to use.
Wikipedia provides a nice overview of different techniques (
http://en.wikipedia.org/wiki/Multi-master_replication
) and also provides a link to another alternative DBReplicator (
http://dbreplicator.org/
).