I also have a super skinny toddler. She's not a picky eater, but she's not that interested in food and only has a few bites of anything. I try to make sure what she does get is full of calories and good stuff and she eats every 2 hrs or so. I don't really let her snack as she seems to fill up on crackers etc and then not eat a full meal!
Here's what I give her (not all at once! might have any one or two of the following):
Breakfast-cereal with whole milk (weetabix, raisin bran or oatmeal), egg, toast, juice
Mid-morning snack-full-fat yogurt, toast with peanut butter or

nutella, banana
Lunch-pasta, ham sandwich, pita and hummus, pb & j, yogurt, fruit, water or milk
Mid-afternoon snack-raisins, cheese, that sort of thing
Dinner-what we're having plus dessert
plus 8oz whole milk before bed (not breastfeeding anymore)
It's hard when you can't use milk or soy--how far-reaching is his milk intolerance? Can he do cheese or yogurt? Hummus is good, avocado very filling and lots of good fat, if he doesn't have allergies nut butters are great--nutella really isn't that bad for you and frankly, children will always eat it.