I made a utility to clean a config file generated by /writeconfig by removing cvars with default value, server only cvars, web ui cvars, and commenting out unused scripts/deprecated cvars.

It also organizes binds by their function.

To use it, extract the contents of the zip file to any folder, double click the executable, navigate to the cfg file you wish to clean up, and it will generate a file called output.cfg in the same folder as the executable.

Input: http://pastebin.com/0EGeHAQP
Script: http://pastebin.com/YPnUpu96
Output: http://pastebin.com/MbYEpRzn

Updated default cvars for December 16, 2015 QL changes
Fixed a bug with whitespace being captured after a cvar name

(v2.0.0 (2015))
Old script files should work but included script has some more features:
removeCvar (got rid of the unnecessary text files)
combinedCvarGroup (groups default and non-default indiscriminately)

Fixed a bug where dragging a cfg file onto the exe did not work properly
Fixed a bug where the layout script file located in the same folder as exe was not detected
*Hardcoded QL default cvars into the program to reduce extra files (in their /cvarlist format to make it easier to change if the occasion arises)
*this removes the ability to use this on other Q3E games with similar syntax by customizing the default cvars, I'll keep older version hosted
Added windows save file dialog box to configure the output filename and save location and utilize favorited windows locations i.e. QL steam directory

(v1.5.1 (2014))
Added section in output for exec'ed config files. Fixing notepad output made an extra blank line on all other text editors, so I reverted it.
Added cvar sections to the layout script, fixed whitespace issues while reading a config file, added option in layout to remove comments or preserve them with original or single spacing. Also, you can now drag and drop a config file onto the .exe to generate an output.cfg (included 3 files (cvars,remove,layout) must be in the same folder as exe)
Now includes "layout.script" to set binds categories and add binds to those categories. Script also contains an option to show/hide unused stuff. Open .script file with text editor to change it.
Default cvars are now stored in cvars.txt instead of default.cfg
Added over 500 default cvars thanks to Lorfa
Detects "vstr" in alias
Added 4 cvars to default.cfg
Detects scripts starting with "set" instead of "seta" only
Output is no longer completely lowercase, stays the same as original.
Now includes "remove.txt" where you can set what substrings will be removed from output.
This version onward should no longer require the redistributable dll.