Here are a couple of sites I used/companies I booked through when planning my RTW trip.
1. DECIDING WHERE TO GO
The City Book: A Journey Through the Best Cities in the World. A Lonely Planet publication. I chose many of the cities I visited because I liked the way their pictures looked in this book.
The Travel Book: A Journey Through Every Country in the World. Another Lonely Planet publication.
*Note: These books can be purchased online at http://www.lonelyplanet.com or http://www.amazon.com
2. TOUR COMPANIES
Intrepid Travel (http://www.intrepidtravel.com/). While I´m happier as a solo traveler, Intrepid gets high marks as far as tour groups are concerned. A native guide helps you get from Point A to Point B (a huge help to me in crazy north India) and gives you a brief orientation tour of each new city. Then you´re free to do as you please and eat where you please. However, if you desire more personal time with the guide, he or she is available to show you around the city.
Israel Experts (http://www.israelexperts.com/). If you´re in Israel, this company offers tours around the country as well as tours to neighboring Jordan. We used Israel Experts to visit Petra, Amman and Jarish.
Hend Harb (email: email@example.com). An excellent, Egypt-based private tour guide that was recommended to me through word-of-mouth.
Eurorail Train passes (http://www.eurail.com/home). Europe has an open-borders policy, and the train connects all major cities. The Eurorail pass is only available to non-EU residents. But note that it can´t be printed out as an e-ticket; it must be mailed to a physical address. Luckily, this can be a European address if you´ve already arrived in Europe.
Hostel World (http://www.hostelworld.com/).
Couch Surfing (http://www.couchsurfing.org/)
*** For more on Logistics read these blogposts.