Acupuncture has been shown to promote healing in peptic ulcers both in animals and in humans (Medical Acupuncture Churchill Livingstone, Edinburgh 1998) perhaps by reducing stomach acidity. In my experience it also often seems to help with hiatus hernia, reflux and dyspepsia, although the mechanism is not clear.
Gastro-oesophageal reflux disease (GERD or GORD) may be associated with myofascial trigger points in the muscles of the belly wall and may also respond well to a more manipulative approach (Travell & Simons' Myofascial Pain and Dysfunction; The Trigger Point Manual Vol 1 2nd ed Williams & Wilkins 1999). Trigger points in the belly wall are linked with colitis and irritable bowel syndrome (IBS) as well and these conditions are often helped. The problem in IBS may be due to a disturbance of serotonin (a neurotransmitter), and some research suggests that acupuncture works to rebalance the serotonin pathway.
Another study which showed the great potential for acupuncture in gut related disturbances was a paper presented at the 4th International Medical Acupuncture Meeting, Barcelona, October 2009 by a Swedish worker, Marianne Reinthal, who has treated 1500 children with colic. Using minimal acupuncture on just one pair of acupoints she relieved the symptoms in 97% of the children, often with a only a couple of treatments.