I'm working on Jordan and Israel for May 2011.
We are a bit tired of the tour groups. We seem to enjoy ourselves more, and remember more, when we are on our own. But it does require a lot of planning.
For Jordan, it is possible to arrange a private tour through a Jordanian tour company. I did some searching on TripAdvisor and found a few companies that do this that get favorable comments. I've been working with Jordan Direct Tours (also called Jordan Select). The website is jdtours.com. On the left of the screen, you will see links both for private tours and for small group tours.
Basically, we started with one of their small group itineraries. Then we customized it to fit our needs. We chose hotels from a list they provided. They also allowed us to opt out of their hotels - for example, I had enough Starwood points to reserve a room in Amman with points (reducing the total cost of the tour). This was all done via email.
For Jordan, I purchased The Rough Guide to Jordan by Matthew Teller. You'll find the book on Amazon. This seems to be a pretty good guide book and I used it as we were designing our itinerary.
Israel is more work since we plan to be independent. I'm working with an Israeli travel agent that was recommended on TripAdvisor. The agent is helping us with hotel reservations and car rental.
If you prefer to use a tour company, I'd also look into Gate 1 travel and Isram World.