This is the folder structure:

./demos/               Demos
./env/                 Skyboxes
./gfx/                 Console backgrounds
./locs/                Location files (i.e. ".loc" files)
./maps/                Custom maps
                       + Colored lighting files (i.e. ".lit" files)
./models/              Model textures
./pics/                HUD textures
./players/             Player models + skins
./sound/               Sounds
./sprites/             Sprites
./textures/            World textures

If a folder doesn't exist, simply create it.

The file "pak0.pak" contains the Quake 2 v3.14 demo (or the full version Quake 2).
The files "pak1.pak" and "pak2.pak" contain the Quake 2 v3.20 point release.
The file "nquake2.pkz" contains the nQuake2 specific files. It can be opened using WinRAR.