I think a simple "thank you" would be plenty and comments like "oh, don't mind the mess" are just self-effacing remarks. But then, I am kind of a clean freak and I take pride in how my home looks so a "your house is so clean" would be a compliment to me the same as it's a compliment to my friend when I tell her that she always looks so nice and put-together.
The remarks I love (not) are the people who come to my house and say things like:
"Your house is so clean, you obviously do not have kids" and then they go on and on about how one can have a clean house or kids, but not both and how they never have time to even wash dishes or vacuum. I'd think if I had kids, I'd want to make sure the house was ESPECIALLY clean because kids (little ones, especially) spend so much time on the floor and putting things in their mouths. I get that there will be toys on the floor and such, but having kids is no reason to let dirty dishes pile in the sink and dirt to accumulate. Of course, part of this is my annoyance at how it seems to be assumed that because I don't have kids I have more than 24 hours in a day, which is another thread entirely.
The best one, though, was my ex's stepmother. The woman NEVER cleaned her house, and anytime she'd come to visit, she'd remark how I must have some type of obsessive-compulsive disorder because the house was so clean. When we'd go to visit her, she'd have to move piles of laundry from the furniture to make room for us to sit (and it wasn't a guarantee that said laundry was actually CLEAN laundry waiting to be folded.) There was clutter and garbage everywhere, the kitchen table was always piled high with dirty dishes, leftover food, and all kinds of carp, and the house smelled BAD. Her excuse? She and ex's father were both out of work and they just didn't have the money to clean.
HUH??? It costs money to fold laundry or put it in a hamper??? It costs money to pick up garbage and clutter?
It costs money to run a dustrag around the house and straighten the sofa cushions??? Who knew???