The tool I work for ( ECMerge ) does this primarily to help you visually combine them visually. You can also save files left / right / ancestors with built-in Javascript engine. ECMerge reads markers for most of the "well-known" source code controls (CVS, git, mercurial, bazaar, SubVersion, Perforce, those that are compatible with previously cited and, of course, their own markers!).
source share