I advise you to read the Wikipedia article on Wavefront .obj file (and MTL), the external links are interesting too, especially the specification, it helps to understand this ASCII file format, its "commands" (v, vf, vn, vt, f, mtllib, usemtl, o, s, g, ...) and its structure.
The other examples I quote can help you to understand how to parse the files and to convert your data into something more "OpenGL friendly" by using a few JOGL classes or more high level utilities.
There are one OBJ loader in JOGL and another one in JOGL-Utils: ObjReader and WaveFrontLoader.
There is the LibGDX OBJ loader too. LibGDX has a non official backend based on JOGL which is actively maintained by @bgroenks, @xranby and me.
You can use JogAmp's Ardor3D Continuation too (which uses JOGL under the hood), you can look at this simple example, its WaveFront OBJ importer (it shows you how to parse an OBJ file) ant its storage (it shows how to store the data into some structures to use them later to draw with JOGL).
N.B: I'm responsible for engine support in the JogAmp community, I'm in the list of the official maintainers and I'm the main contributor of JogAmp's Ardor3D Continuation which isn't a fork of Ardor3D but a "continuation". The development of the legacy Ardor3D was stopped in March 2014 according to its main developer Renanse as stated here on his blog.