Some years ago, John Lavagnino and I wrote the EDMAC
software for typesetting critical editions. EDMAC was an application for use with plain TeX. Later, adaptations were made to allow EDMAC to work with LaTeX etc. More recently, the ConTeXt package, also based on TeX, has been developing methods for handling critical edition typesetting.
Idris Hamid, Colorado State University, recently gave this talk at the TUG 2007 conference, San Diego, about doing critical editions using ConTeXt.