Give them separate rows. Be creative with seating at the reception. Just make sure everyone's taken care of and feels equally important. Just like you'd choose someone to do a reading or help you shop for favors, give each parent a special role in the wedding. Let them know you've chosen something special for them to contribute to your big day.
Little things can make a huge difference.
If you're dealing with parents who will ingnite a fight upon laying on each other, chances are you'll know to keep them as far apart as possible. But make sure they know you're thinking about how this will affect them too. Spend the extra money on the photographer's time and get pictures of every scenario. While it's great to have the entire family photo, mom might not want to display the ex on the mantelpiece. Get one with the two of you with each parent, parent and spouse, you with your mom separately, you with your dad, etc.