I also use paper charts to look for these. I find that the WikiTree Ancestors list (at http://www.wikitree.com/treewidget/LNAB-xx/9 is reasonably easy to skim -- and of course electronic files can be searched for other instances of a name that I think might be a repeat. I'd love to have an automated tool, but I have a hunch that this would be a major technical challenge.
Related to this, my sister recently pointed out to me that in cases of endogamy, the WikiTree Find Relationship algorithm (which is a really awesome tool) doesn't always find the shortest path to an ancestor. My example: