By default the entire event will be written out, except for any collections flagged as transient when they are added to the event.
transient.java
List myCollection = new ArrayList();
// Fill collection
event.put("MyCollection",myCollection);
event.getMetaData(myCollection).setTransient(true);
In addition when creating an LCIO driver it is possible to specify either what collections should be written out, or which collections should not be written out.