Far as I know thats it, usually flying thru Miami is cheaper...oddly enough.
I am planning a trip to Central America and the Caribbean at the end of the year. I am just looking into getting from Panama City to Kingston in the Jami. The only direct flight I have found, which is on COPA is over $600(US) and the cheapest I have found is about $450 on AA but it goes via Miami which seems like a very long way around.
Obviously budget is an issue for me. Just wondering is there any other route that would be cheaper. Two leg journey's aren't an issue, but obviously 12 hour stop overs wouldn't be ideal.
Any help would be greatly appreciated.

As you already know, COPA is the only direct option. Cayman Airways changing planes in Grand Cayman is another alternative. Other alternatives go through the USA (a big detour, I know); e.g. Spirit Airlines changing flights in Fort Lauderdale.
Keep in mind if you are not a US Passport holder you need to arrange for a Visa waiver to transit in Miami/USA.
If you find fares to Kingston KIN too expensive try to fly to Montego Bay MBJ (again with COPA). Return fares are cheaper than single fares.
Also do look for COPA holiday programmes (COPA Vacations) to Jamaica, maybe you'll find Airfare Transfers + Hotel Meals for the same USD600 and will be able to change the return date and extend the stay on the island.