AdQuedit: The Quake Workstation aims to be the center of any Quake modding workflow. Its most obvious function is in being a general front-end for browsing through your Quake files and launching other mod tools. This is hardly its only feature, however.
Where AdQuedit most comes in handy is in graphics and textures. With it, you can replace and extract textures, regenerate mipmaps, replace model skins, create sprites, and modify the palettes and colormaps the game uses. AdQuedit can also extract entity lists from maps for editing in a program like EntEd, allowing for easy patching of a BSP without recompiling.
Also available for download is the little-seen AdQuedit manual, in case you're curious as to the ins and outs of the program.