On the West Bank, a tour can be a good way of both getting oriented and staying safe.
Green Olive Tours (www.greenolivetours.com) Offers a wide variety of highly political but insightful day trips and multiday tours in both the West Bank and Israel.
Hijazi Travel (http://hijazih.wordpress.com) Owner Hijazi Eid specialises in West Bank hiking and trekking, as well as city tours.
Alternative Tourism Group (www.atg.ps) Culture, religion and politics, as well as walks along the Nazareth-to-Bethlehem Nativity Trail.
Abu Hassan Alternative Tours (www.alternativetours-jerusalem.com/) Offers both 'political' and 'touristic’ day trips.