The seeds are eaten straight from the pod or can be toasted and sprinkled with a little lime and salt. I have had them toasted also with a little finely chopped white onion mixed in and quite good they were.
There are two varieties, the green which is common and a red which is less common. The red is more garlicky. The Spanish substituted guaje for garlic, and very fresh green sometimes and the red always when I've tried it (which is only a few times) are indeed garlicy.
For this reason, perhaps, guaje is used in mole, if by mole one simply understands sauce. A sauce made with guaje is called, duh, guaxmole (okay, the spelling is a BIT tricky).
A recipe for Chicken in a tomato-guaje sauce (that appears without attribution although the writer makes reference to a connection to the kitchens at Frontera Grill and Topolobampo) is here:
http://www.pepperfool.com/recipes/chick ... asado.html
I also found a recent (this month) reference datelined Coyotopec, Puebla regarding the state government's interest in promoting the cultivation and marketing of red guaje as a means of economic development for a group of Mixtec women in that state. The article references a "tortitas de guaje" made from ground guaje seeds that I have not heard of, but it sounds interesting. I quite like guaje and will purchase them just to munch on.