Comitan receives only a fraction of the tourist traffic that San Cristobal sees, so if you enjoy being immersed in local culture, you might enjoy spending a day or two in Comitan. It makes a sensible stopping off point, especially if you are heading to or from Guatemala. Comitan has good facilities, with plenty of ATMs, cafes, restaurants, retail outlets and pharmacies.
For the main attractions, such as plazas, churches etc, exploring by foot is fine. There are colectivos that ply the main routes, ferrying passengers between the main plaza and bus stations etc.
Comitan is a pleasant and affluent colonial style city that can be a nice alternative to San Cristobal de las Casas. It has a very laid back and friendly atmosphere, with several nice plazas and beautiful churches. It is a good launching off point for a number of sites in Chiapas, and is on route from and to Guatemala.
Stroll around the main plazas, explore the city by foot, enjoy the laid-back atmosphere, and visit one of the free museums in the streets which surround the town centre.
There are plenty of restaurants around the main plaza opposite the church. If you want cheaper food you can find some basic tacos etc in the market (walk past the the church in the main square on the left side and the market will be on your right). There are also a few small street vendors around for snacks like tacos, etc. One calle from the main plaza, there is an excellent Italian cafe, serving fantastic coffee and tasty authentic Italan pastas etc.
There plenty of mid-range accommodation options around the main plaza.
There are several cheap, fast and modern internet cafes around the calles off the main plaza.
OCC and several private mini-bus operations service surrounding locales, including the Mexican-Guatemalan border and San Cristóbal de las Casas (both less than two hours, approx 50.00. Terminals are located on Boulevard Belisario Dominguez Sur.
Guatemala- Take a collectivo to Ciudad Cuauhtémoc where you will report exiting the country at the immigration office. (Exit Tax : M$390, September 2016) From there, take a taxi for 10 pesos to go to the Guatemalan Immigration Office. After you finish immigration process, DON'T take the van waiting just in front of the office - they don't take you all the way to the destination and will charge you about 400 pesos. Go ask around for Chicken bus to your Guatemalan destination.
Chucumaltik - a cenote about 20km from Comitan. Take a 'Uninajab' combi from the Tzimol combi station (2 blocks west from the park). Ask the combi driver where to get off.
Chinkultik - a pre-Columbian city that dates back to the third century close to Lagunas de Montebello. Take a Lagos de Montebello combi from the main boulevard and asked to be dropped off by the ruins. From the main road, motor taxis (MX$20) take you to the ruins. Free entrance.
El Chiflon - waterfalls about 30km from Comitan. Take a collectivo to Tzimol. It takes about 45 minutes and 45 pesos. El Chiflon's entrance fee is 30 pesos and you can take a motortaxi from the entrance for 10 pesos. [2/18/2018:] Tzimol is only halfway to the falls. Take a Tuxtla bound minivan at the TPA terminal (next to the San Cristóbal minivan terminal on the boulevard, a bit north of the OCC terminal on the other side of the street) and ask for El Chiflón. They will drop you at the entrance. 50 minutes, 35 pesos, first bus at 05:00, leaves every 20 minutes.
Lagos de Colon - river and lagoon system near the Lagartero ruins. Take a "Comalapa" combi from the main boulevard and asked to be dropped off for Lagos de Colon. From there, take a taxi (MX$50).
Lagunas de Montebello - a collection of 59 lakes famous for their striking colours. Take a Lagos de Montebello combi from the main boulevard. It costs about 45 pesos and takes an hour or so.
Laguna Miramar: To get to the jungle lake of Laguna Miramar from Comitan it is necessary to take a colectivo to the small town of Las Margaritas from where there is a second colectivo to San Quentin (6 hours). It is a 1 km walk from San Quentin to the village of Emiliano Zapata from where you can hire a guide to take you through the Lacondon jungle to Laguna Miramar. For colectivos to Ocosingo, there is a different terminal on the other side of town. You should probably take taxi (its around a thirty to forty-five minute walk, ask locals for directions).
Las 3 Tzimoleras - a private eco-ranch in Tzimol, a municipality 12km from Comitan de Dominguez. The name 'Las 3 Tzimoleras' refers to the 3 amazing waterfalls located within the ranch which is mostly lush forest with bare basic facilities. Eco-adventure tours to the waterfalls include activities like canyoning, camping, horse-riding, hiking and ATV. Visitors can also swim in the many natural pools along the river. More info: 
Tenam Puente - Mayan ruins about 15km from Comitan. Direct combis from the Tenam Puente station (approximately 3 blocks west from the park).