Graphical Replacements
Skins
Map Textures
A good place to start is with the Quake Re-texturing Project. It covers all the stock quake textures, it will instantly improve any maps using the defaults.
Individual Maps
Install: Unzip the folder into quake/fortress/textures/
Example: 2fort5.zip should be unzipped into quake/fortress/textures/2fort5/
Protip: Use map grouping command in EZquake to load one set of textures across multiple maps.
Example: mapgroup 2fort5 2fort5r 2fort5sta 2fort5fel ; mapgroup aztec1 aztec1sta aztec1fel miniaztec1
Models/Weapons
Upgraded, but true to Quake graphical (ammo/armor/health/etc) replacements. Download textures.pk3
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.