This tutorial is what I used when learning modern OpenGL
http://web.archive.org/web/20140209181347/http://www.arcsynthesis.org/gltut/I use the NEWT API in jogl to capture mouse events. THen I have to do some maths to get from mouse coordinates to the coordinate system the mesh is defined in, then you can modify the mesh.
So you can look at the JOGL examples also, they have a lot of useful code you can use to listen to mouse event et c.