I've been working on this for hours, same issue. I've ruled out pretty much every documented control that has anything to do with email notification, and I do not think this is something that can be controlled through Setup menus or through Apex.

To recap: the problem is that in all other instances where case ownership is changed, the email notification to the new case owner is not sent. But when the trigger runs that reassigns a case to a new owner, the email notification is sent. I don't want this to happen.

Here's the code I've written for the trigger. You can see I've tried the Database.DMLOptions methods to prevent the auto email. Based on the fact that these methods fail, I think they do not have any bearing on case email notifications, (which is probably why emails notifications on case updates are not listed in the documented events that DMLOptions are meant to impact).

trigger caseAction2 on Case (before update) {
	Set<Id> setOfCaseIDs = new Set<Id>();
	Database.DMLOptions dlo = new Database.DMLOptions();
						dlo.EmailHeader.triggerUserEmail = false;
						dlo.EmailHeader.triggerOtherEmail = false;
						dlo.EmailHeader.triggerAutoResponseEmail = false;
	for (Case d : trigger.new){
		//test that the case.OwnerId in the new set is not the same as the case.OwnerId in the old set. If it is, <exit> (break or return?) 
		if(d.ownerId == Userinfo.getUserID() || d.ownerId != Trigger.oldMap.get(d.Id).OwnerId){			
			break;
		}
		else{		
			for (Case c : Trigger.new){
				setOfCaseIds.add(c.Id);
			}
			Map<Id, Case> mapOfCaseIDs = new Map<Id,Case>([SELECT Id, OwnerId from Case Where Id IN :setOfCaseIds]);
			for (Case c : trigger.new){
				//if the map set contains the case C
				if(mapOfCaseIDs.containsKey(c.Id)){
					//and the case owner ID is not the active user
					if(mapOfCaseIds.get(c.Id).OwnerId != Userinfo.getUserId()){
						c.setOptions(dlo);
						c.OwnerId = Userinfo.getUserID();	
					}
				}
			}
		}
	}
}

 This thread is several months old and if anyone has found a solution to it I'd love to hear about it.