Are there tools to find a subset of references shared by two or more publications?
The process of finding the intersection of the references in a given set of papers is known as bibliographic coupling and was first proposed by M. M. Kessler in 1963 in a paper that sadly remains locked behind a paywall 52 years later. Kessler was thinking about doing this for pairs of papers but of course you could do this for an arbitrary number. What might also be interesting would be to look for the set of papers reachable by following citation trails backward in time through any number of steps. 

I am unaware of any on-line tools that perform this type of comparison for you, though it would not be hard to build such a thing if you had access to a big enough citation graph.