Well, you got And Then There Were None. I'd suggest the rest of Christie's catalog, but none of them ever quite reach that level again. The Murder of Roger Ackroyd comes closest imo.
Looking at my bookshelf, the only other book that matches the description is The Westing Game by Ellen Raskin. Not a murder mystery in the strictest sense, but there is a dead body that may have been murdered.
It works on three levels:
1. Mystery. This is just a damn good whodunit. Raskin's approach is to have sixteen detectives all following different investigations, so that no matter how silly or outlandish, someone is hunting down a lead. Every plausible lead and several that aren't get someone actively hunting them down, so there's never a point where the reader figures out the answer because every other avenue is drying up.
2. Comedy. Every lead gets someone hunting it down, no matter how crazy it may seem. This makes for some varied and absolutely wonderful laughs.
3. Drama. Although a comedic mystery on the surface, there is much more to this story than immediately apparent. Raskin is making a commentary on the American Dream, and what the United States as a nation represents. It is clear that Raskin loves her country and what the nation has given her, and an examination of its deeply ingrained racism and classism that divides it.
1. Although this is mostly an intelligent depiction of racism, there is one character that is a straight-up offensive stereotype, and she stands out all the more compared to the rest of the cast. Although several characters begin as fairly racist caricatures, Raskin uses these first impressions to turn our initial views on their heads. In the case of Sun Lin Hoo, she fails miserably. Madame Hoo is the only character who doesn't speak English and so we are rarely given any windows into her mind. When we do, the character shows herself to be infantile: apparently, not being able to speak English means that she doesn't know what Mickey Mouse is or how much every day objects are worth. Sun Lin Hoo is the one blight (and a major one) on an otherwise excellent novel.
2. For readers who aren't American, I'm not sure how much sense a lot of the references will make. This is a book HEAVILY steeped in American culture, and I've seen people say that they missed major clues simply because they weren't intimately familiar with the exact coordinates of the Statue of Liberty (I'm making that up, but that's the kind of knowledge this book *would* expect you to have memorized ).