Preheat oven to 375º.
Lightly spray or grease ramekins with olive oil. Line a baking sheet with aluminum foil (to prevent messes while baking.)
Using a mandolin or a sharp knife, slice off the ends of the eggplant, zucchini, squash, and tomatoes. Thinly slice them into 1/8-inch rounds.
Spoon 2 tablespoons of marinara into the bottom of each ramekin.
Make a layer of eggplant, a layer of zucchini, a layer of squash, and a layer of tomatoes. For the last layer, use whatever remains. Sprinkle salt and pepper over top of each ramekin, then evenly divide the remaining marinara sauce equally and spoon over top.
Place ramekins onto baking sheet and cook for 40 minutes.
Remove and allow to cool, then garnish with fresh basil if desired.