The Royal Mummies. The mummies of Egypt's New Kingdom pharaohs — the actual bodies of Ramesses II, Seti I, Thutmose III, Hatshepsut — were long the most extraordinary thing here, and the collection has been reorganised in recent years and partly relocated to a purpose-built hall at the National Museum of Egyptian Civilisation in Fustat. Check where it currently sits before you plan around it, because it is worth planning around.
The Amarna room. Akhenaten's reign produced Egyptian art unlike any other period — elongated faces, informal family scenes, a naturalism that appears once and never returns. The colossal statues of Akhenaten here are among the strangest objects in Egyptian art.
The Old Kingdom sculpture. Rahotep and Nofret, the seated scribe, the Sheikh el-Beled, Khafre with the falcon behind his head — these are the foundational works of Egyptian art and they are here, at eye level, usually with nobody standing in front of them.
And the building itself is now a historical object. It is the last surviving example of how a great archaeological collection was displayed a century ago, and once Egypt finishes moving material out to newer museums, that atmosphere will be gone.