In addition to the 1-day organized trip, those interested in individually joining a guided tour from their hotel, may want to look, for example, at the reviews on TripAdvisor:

http://www.tripadvisor.com/Attraction_Review-g293983-d1946663-Reviews-Guided_Tours_Israel_Day_Tours-Jerusalem_Jerusalem_District.html

or the following:

Egged Tours www.eggedtours.com

Mazada Tours www.mazadatours.com