Preheat oven to 300ºF. Line 2 large baking sheets with foil.
In a large bowl, mix oats, nuts and wheat germ. In another bowl, whisk brown sugar, molasses, oil, vanilla, salt and spices. Stir molasses mixture into oat mixture. Divide between 2 baking sheets, spreading evenly.
Bake granola until browned, 50 to 60 minutes, stirring every 15 minutes. Halfway through baking time, switch baking sheets from top to bottom and front to back. (Granola will turn very dark brown from the molasses.) Remove baking sheets and transfer granola to a large bowl; let cool, stirring occasionally. Toss in raisins, if desired.
Just before serving, assemble parfaits: Spoon about 3 Tbsp. granola into each of 8 small bowls or parfait glasses. Top each with 2 to 3 Tbsp. yogurt. Repeat layers once. Serve immediately. Store extra granola in an airtight container in the refrigerator for up to 2 weeks.