Some service providers detect an idle connection to the database and terminate the link. This is done at the firewall level. For example, microsoft Azure does it with SSH and MySQL connections.

So every couple of minutes when I try to query, I get a message that the connection was terminated. If I don't have timeouts set for my JDBC connection, it sometimes hangs indefinitely until I terminate netbeans and restart.

I've used a number of clients (beaver SQL) and they have a nice option to query the database every X seconds. You set the interval and enter the query. It could be something very silly (SELECT NOW()). But the effect is that the connection stays alive and you don't have to worry about firewalls terminating the connection. This would be a superb feature to have (unless there's some other way that I don't know about).