I prefer to freeze unbaked mac and cheese. I am very sensitive to the smell of foods from the freezer and in general prefer to freeze ingredients over the end product.
To Judy Goldberg sub question, better to freeze unnamed or baked? AS long as the components are cooked once, about equal, with a slight pref for unbaked, so your dish is not overcooked.
I always wait until its cool and put it into a freezer/oven safe dish that way when your ready to use you can defrost in the fridge and pop in the oven. You may need to add some milk before reheating so that it doesn't dry out.
If freezing in single-serving sizes, I have found it very useful to wrap each piece in plastic wrap before shoving the lot in a large freezer bag. It cuts way down on freezer burn and makes is much easier to pull out one serving at a time.
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