Graphical Replacements
Skins
Map Textures
We can post links to individual map texture replacements, but a good place to start is with the Quake Retexturing Project http://qrp.quakeone.com/, since it covers all the stock quake textures, it will instantly improve any maps using the defaults.
Individual Maps
Include bump/norm/gloss/luma/glow textures where available for engines that support them.
Models/Weapons
A million available..for example at http://gfx.quakeworld.nu
Sample MegaTF model pak here: Sample model Pak
Skyboxes
Install: Unzip the files into your quake/qw/env folder.
Load a skybox: Type "loadsky <skybox name>" in the console.
Disable skybox: Type "skybox 0" in the console.
Audio replacement
Not graphical, but an upgrade to all of the original quake sounds.http://gfx.quakeworld.nu/details/384/mindgridaudio-high-resolution-quake-1-sounds/
Use s_khz 44 in EZQuake.