Mario x Mario. It's the best couple ever. You can even see the couple in my signature and the boxart for Super Mario Land. Nothing beats a couple with shared beliefs and interests. They also look perfect, as if they were made for each other. They fit.
I'd also vote for Luigi X Warp Pipe, too. You can see how cute they look together. They're both green and tall and proud as well. They're also made for each other as well.
Wario X Honey Queen are a profound pair. They are both fat idiots that no one likes, so when they're together, it's easier to take both of them out in a bombing.
MSS Sea Star X Daisy Cruiser are the perfect shipping. There is no better shipping when there are two actual ships involved.
As you see, I'm really in to shipping.