Egypt has endless options, and  - to put it bluntly - a lot of the hotels are not very good! In the different areas (mainly Aswan, Cairo and Luxar) there are only a handful of hotels which we are confident offer an excellent experience, and therefore these are the only ones we recommend. We have sorted the chaff from the wheat for you, so take a look at the below options and see which destinations and hotels grab you.
The below hotels are the iconic ones, which have a good standard of luxury and quality throughout. In Cairo, Mena House is a fantastic option as you can admire the pyramids from the comfort of your room. It is convenient and luxurious and definitely the place to be in Cairo. On to the ancient tombs and temples of Luxor, if you are venturing here it has to be Winter House which is the staple hotel in the region – it is not hugely glitzy, but there is a certain amount of charm in its rustic yet comfortably luxurious walls as this hotel is hugely historical, so would suit any traveller interested in the regions history. On to the peace and tranquillity of Aswan, it would be a shame not to base yourself in a hotel which epitomizes just this; therefore Old Cataract is the place to stay here.

For something a bit different, there is the Sun Boat Cruise which takes you on a historical trip back in time between Aswan and Luxor on this fabulous Nile Cruise. This is a 4 night trip, and costs $540 per person per night.
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Mena House - Giza, Cairo

Our View

Mena House is the place to stay if you are in Cairo ostensibly to see the pyramids; mainly because you can, from your balcony.
Luxurious, comfortable, quiet, and convenient, Mena House also has a hint of its history to create an atmosphere to allay too many ‘Big Impersonal Hotel’ feelings, and although it is no longer run by the Oberoi, we very much hope that nothing will change.

(It is also worth mentioning their memorably wonderful Egyptian breakfast... think figs, fresh honeycomb, melon and dates, all enjoyed in a sun-dappled dining room with old lattice wood shutters).  
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    Cost: $150
    Old Cataract - Aswan

    Our View

    We have always loved the historic charm of the Old Cataract, with its unparalleled Nile-side location, elegant terraces and Agatha Christie suite, although it was, in the past, a little dusty and run down. But now, after four long years of meticulous, painstaking renovations, the Sofitel Hotel group have reopened this fabulous hotel, and it is a real treasure. The swimming pool and sun deck have been lavishly extended, and the rest of the hotel is restored to its former glory. 
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    Cost: $150
    Sun Boat III - River Nile

    Our View

    We love the idea of cruising down the Nile, seeing the best of Egypt's sights on the way, but we don't like big cruise boats, crowds or any kind of tacky discomfort. Sanctuary Sun Boat is ideal; comfortable, small and completely the right vibe. Hooray for the less showy and altogether more attractive options... with small pool, loungers, library and restaurant to write home about...
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    Cost: $150
    Winter Palace - Luxor

    Our View

    The Winter Palace is THE place to stay in Luxor, despite the fact that it really has seen considerably better days. It is falling down, the curtains are threadbare and the service is distinctly idiosyncratic... but it is hugely historic, and brilliantly placed for exploring Luxor. We enjoy the waterfront, the gardens and pool too, especially after a hot day...
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    Cost: $150
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