In a recent commentary, the authors provide a list of the most commonly cited digestive disease articles from 1967-2007.  (Gastroenterol 2013; 144: 673-76)

The top three:

1. Manns, M, et al. Lancet 2001; 358: 958-65. This study compared peginterferon alfa-2b with ribavirin against interferon with ribavirin for hepatitis C
2. Fried M, et al. NEJM 2002; 347: 975-82. This study examined the use of peginterferon alfa-2a with ribavirin for hepatitis C
3. Marshall B, Warren J. Lancet 1984; 1: 1311-15.  This study identified a bacteria (now called Helicobacter pylori) as a cause of ulcers and gastritis.

http://dx.doi.org/10.1053/j.gastro.2013.02.013