San Juan Chamula
There are collectivos all day from San Cristobal. Although you do not need to go with a tour -- it takes about twenty minutes in a collectivo -- taking a guided tour does help give you context for what you see in the villages, and with a good guide you really get a feel for daily Maya life that you could never gain alone.
Most of the agencies in San Cristóbal offer half-day tours to Chamula and Zinacantán that leave at 9.30 AM. If you're looking for the flexibility of a private tour, Cielo y Tierra Tours has an excellent guide, Alex Aranda. Their tours also include a fascinating hike (optional) in the hills surrounding Chamula. A private tour for two costs $750 MXN pesos each person. For further information, visit their website. 
It is easy to walk anywhere in San Juan de Chamula.
The church in San Juan Chamula is a must see. Here the Mayan traditions are blended with the ideas of Christianity. There are saints representing gods and the people go to church to be healed rather than to pray for salvation. Worship is a private family affair rather than a community responsibility. Please do not take photos in the church -- this is highly offensive to the people and could result in you losing your camera.
There is a big market in front of the church -- you can buy locally made handicrafts of wool. They make purses, skirts, dolls, ect. The town itself is extremely poor and it would be helpful if you supported the community and purchased some of their handmade goods.