Upper Egypt is, in fact, the part of the country that lies in the Nile Valley to the south of Cairo. Most of us think north when we think "up," and for this reason, the name seems counterintuitive. Remember, however, that the Nile flows downhill from its headwaters and the Ethiopian Highlands. As you go south from Cairo, you're literally going uphill into Upper Egypt.
The area, and specifically its biggest town, is the richest and most exciting part of the country for people with an interest in Egyptology and Ancient Egypt. Luxor, the biggest town in Upper Egypt, lies near the ancient city of Thebes, which was the religious and cultural capital of Ancient Egypt from the Middle Kingdom onward. The area around Luxor contains some of the best-known and most spectacular monuments of the ancient world including the Valley of the Kings, with its densely packed clusters of magnificent tombs that include the most famous of all ancient burials, the final resting place of Tutankhamun. It also includes Karnak Temple, the Temple of Hatshepsut, the Valley of the Queens, and the Valley of the Nobles -- the list can go on and on, but words fail to capture the richness and variety of the ruins and sites here.
As you head south, you're not just heading into Egypt's past, but also away from her Mediterranean face and toward her African roots. South of Luxor, in Aswan, you'll find yourself in the ancient land of Nubia. This country, which had a history as long as Egypt itself, was first subsumed to the Egyptian state in antiquity and then all but obliterated by the construction of the Aswan High Dam in the 1960s and '70s. Apart from some magnificent monuments of its own, which include Abu Simbel and the Temples at Philae, Aswan is notable for its relaxed way of life. One of the high points of any trip to Egypt must be a few hours aimlessly crisscrossing the Nile at sunset near Aswan, where the dunes of the desert come almost to the water and the warm, fragrant air blows the scent of gardens across the valley.
The best way to access the sites of Upper Egypt is to fly from Cairo or, indeed, direct from Europe. If you're short on time, stick to Luxor and its immediate surroundings, as this is where the highest concentration of sites is. If you have a little more time, consider taking in Aswan and Abu Simbel by air or even taking a 4-day cruise between the two towns, which will open up the ancient sites along the riverbanks to you as well. One excellent option is to fly from Cairo all the way to Abu Simbel in the morning, and return to Aswan after a couple of hours at the lakeside monument. Planes go via Aswan, and it is possible to have your bags offloaded on your way through so that they're waiting for you on your return. From Aswan, the options are to stay a while or head back to Luxor by air or -- my preference -- cruise boat.