This is the recipe for low-fat mac and cheese that I always use (but minus the onions because my childhood memories of mac and cheese don’t include chopped onions. But hey, it’s your choice )
The key is to use fat-free milk versus whole milk, and reduced fat cheddar cheese versus regular
I suggest extra sharp cheddar cheese, since reduced fat cheese can sometimes dumb down the flavor.

Hope you like it!

Low-Fat Macaroni and Cheese

1/2 cup fat free milk
1 cup 1% cottage cheese
1/4 cup finely chopped onion
2 TB grated Parmesan cheese
1/4 tsp. salt
Ground black pepper, to taste
3 cups cooked elbow macaroni
1/2 cup shredded reduced fat Cheddar cheese, divided

In a blender, combine the milk, cottage cheese, onion, Parmesan cheese, salt and pepper;
cover and process until smooth. Pour into a bowl; stir in the macaroni and 1/4 cup cheese.

Transfer to a 1 quart baking dish coated with nonstick cooking spray. Sprinkle with remaining
cheese.

Cover and bake in a preheated 350° F., oven for 30 minutes. Uncover; bake 5-10 minutes longer
or until edges are bubbly.

Yield: 4 servings.
References :
http://famousrecipes.wordpress.com/2007/07/28/low-fat-mac-n-cheese/

Just make it yourself and use fat free milk and lowfat velveeta.
References :

The main ingredient for a mac and cheese is of course the cheese sauce. A simple cheese sauce for a baked mac and cheese includes milk, butter, flour, and cheese.

Here’s the recipe I use (the fattening recipe):

4 TBSP butter
4 TBSP flour
2 tsp paprika
1 1/2 c. milk
1 to 1 1/2 c shredded Cheddar cheese
2 c. elbow macaroni (3 cups if you use large elbow macaroni)

Preheat oven to 350.

Cook macaroni according to package directions.

Melt the butter in a sauce pan over medium heat. When melted, add the flour and paprika. Whisk until completely mixed and let cook 1 min. Add milk slowly, whisking as you do so to prevent lumps forming. Lower heat to low and let mixture simmer for 5-10 minutes, whisking occasionally, until thickened. Turn off heat and stir in cheese. The amount you add depends on how cheesy you want your mac and cheese. Once melted, add the mixture to cooked macaroni and bake in a 2-qt casserole for about 30 minutes.

That’s the basic recipe. Since you asked for low-fat, you can use less butter (or margarine if you prefer), low-fat or skim milk, and low-fat cheese. If you lessen the butter, you also must lessen the flour. The flour and butter have to be equal amounts otherwise your sauce will be either too thick or too thin. Also, if you can find it, substitute the macaroni for a whole wheat macaroni. If you can’t find low fat cheese, then use less cheese in the sauce.

Eating mac and cheese, either low-fat or regular, for one night will not break a diet. As a matter of fact, it adds to it because you have the grains and dairy in one meal. Just don’t eat enough to feed a family as my recipe above does.

Enjoy!
References :

•Crock Pot macaroni and Cheese

1 1/2 cups milk
1 15-ounce can evaporated milk
1 large egg beaten
1/4 tsp salt
Large pinch of black pepper
1 1/2 cups medium or sharp cheddar cheese shredded
8 ounces elbow macaroni (about 2 cups)
2 Tbls grated parmesan cheese

1. Coat the slow cooker with nonstick cooking spray. Combine evaporated and regular milks, egg, salt and pepper in the cooker and whisk until smooth. Add the cheese and macaroni, gently stir with a rubber spatula to coat evenly with the milk and cheese mixture. Sprinkle the parmesan on the top.

2. Cover and cook on low until the custard is set in the center and the pasta is tender, 3 1/2-4 hours. Do not cook more than 4 hours, as the sides will dry out and burn.

Note: If you want to make this a low calorie dish you can use lowfat or skim milk, and evaporated skim milk.
References :