ReMESH

The overall architecture and algorithms implemented in ReMESH are described in the following paper:

Marco Attene and Bianca Falcidieno
"ReMESH: An Interactive Environment to Edit and Repair Triangle Meshes"
In Procs of Shape Modeling Internationl (SMI'06), IEEE C.S. Press, pp. 271-276, 2006.

ReMESH is citeware, which means that if you use it for your research, you should acknowledge it and cite the paper.

Take a look at the user manual to know more about the software and about the algorithms implemented.

There is also a short tutorial by Jurrian Hartveldt explaining how to use ReMESH to produce a watertight model starting from a polygon soup.