I grind them fresh and put them on my cereal just before I pour on the soymilk, most commonly. I also mix them into hot cereal just before eating, into smoothies and yogurt (I buy soy yogurt and kefirs).
I also sprinkle them on salads if I didn't get any with breakfast. I have recently learned that walnuts also have a lot of those good omega-3 fats, so sometimes I use those on salads, hot cereal and yogurt just for variety.
I've heard heat is bad for the oil, so I don't cook with them. I don't put flax seed in pancake batter, quick bread, etc. But with the choices I listed above, I can manage to eat them almost every day.
I eat about 1 1/2 to 2 tablespoons, which is about 70-80 calories.