ToMATo: a Topological Mode Analysis Tool
Originally found here, with GPL3 license: http://geometrica.saclay.inria.fr/data/ToMATo/
I may eventually get around to sticking an API on this so it can be called from a higher level programming language.
Original paper is "Persistence-Based Clustering in Riemannian Manifolds" Frederic Chazal, Leonidas Guibas, Steve Oudot, Primoz Skraba Can be found here for the moment: http://ailab.ijs.si/primoz_skraba/papers/clustering.pdf
Nice video lecture by Dr. Skraba here: http://videolectures.net/solomon_skraba_pbc/