Here are some travel companies that I've either traveled with or who I'm considering using for a future trip.
Contiki - Group tours for 18-35 year olds. Large group tours for young people, great for those traveling alone or who are less experienced travelers who don't want to spend a lot of time planning. In some areas the tour groups are smaller sized - Egypt, South America and Asia.
Context Travel - Scholar led walking tours of the worlds Cultural Capitals. Small and private tours of some of the worlds major cities - NY, Paris, London, Florence, Philadelphia, Budapest, Athens, Naples and many more
Intrepid Travel - Small group tours that range from 1 day to months in length. They're best known for their tours in less developed nations, but do have tours around the world. They emphasise the use of local transportation and accommodations, lots of free time and unique local experiences. I know several people who have toured with them and would absolutely tour with them again.
G Adventures - Formerly known as Gap Adventures they specialize in small group tours. They pride themselves in using local transportation and unique local stays. I know several people who have toured with them and all have had wonderful things to say about them