My sister and I booked a private 5-day tour of Oman with Sunshine Tours and are very pleased with how it went. Mohammed was very responsive in building an itinerary and all communication before our trip, and our guide, his brother Khalid, was knowledgeable and personable the entire time. This is an all-Omani company and they are clearly passionate about their country. Service is also top-notch: Mohammed even invited us to dinner while we were in Muscat, Khalid took us to lunch at his house on our last day, and we were picked up at the airport even though we weren't beginning the tour for three days. Truly above and beyond.
We got to see a great variety of sights: sea, desert, mountains, wadis. During the tour, accommodations were basic but clean, the 4WD was clearly well-kept, and all three meals a day were included (not the case with other companies, which also often charged more for similar itineraries). One more nice touch: Sunshine did not require payment until departure. I checked with a couple of other companies that wanted me to wire a substantial sum as a deposit. I wouldn't have a problem paying a deposit with a credit card, but was uncomfortable wiring so much overseas without any buyer's protections on my end.
Their website focuses mostly on shorter tours, but definitely also contact Sunshine if you're interested in a longer tour. They were fantastic.