Luxor is the big one really. Everyone thinks pyramids and they are great but Luxor is blew my mind.
Get to Abu Simbel in the south. It's a short flight/day trip and well worth it.
If money allows for it, take a Nile cruise. It's a great way to see Egypt.
In Cairo, the museum is excellent and the living cemetary is too weird to be missed. The Mohammad Ali Mosque is good to see as well.
Enjoy, it's a great place. Oh, and at least when I was there last, get used to seeing a lot of soldiers in the streets. And if you are a woman or
traveling with a woman, watch for wandering hands!