Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Eilat (60% of total searches to Negev Desert). The next most popular destinations are Aqaba (20%) and Sede Boqer (12%). Searches for hotels in Mitzpe Ramon (8%) are also popular.
KAYAK users have found double rooms in Negev Desert for as cheap as $10 (Aqaba) in the last 3 days. The average price is $219.