After migration to MacOSX 10.11 "El Capitan", how to run simple utilities such as "texdoc" and "kpsewhich"?

You can not use /usr/texbin anymore. This is a final change. Every program relying on that link needs to be fixed. I think this is what Herb Schulz' file also tries to say.

Another change is that /usr/sh won't run non-signed programs anymore. So the /usr/sh pdflatex that emacs is trying won't work:

#/bin/sh pdflatex
/Library/TeX/texbin/pdflatex: /Library/TeX/texbin/pdflatex: cannot execute binary file

while:

#pdflatex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) ...

This may be Apple's fix for recent reports of Gatekeeper breakouts.

This problem can be caused by some leftover junk from previous versions of TeXLive which at one point added the path /usr/texbin to the /etc/profile file (the global /bin/sh profile).

The default /etc/profile on current version of the MacOS should be the following:

# System-wide .profile for sh(1)

if [ -x /usr/libexec/path_helper ]; then
        eval `/usr/libexec/path_helper -s`
fi

if [ "${BASH-no}" != "no" ]; then
        [ -r /etc/bashrc ] && . /etc/bashrc
fi

If your /etc/profile contains code to add /usr/texbin to the PATH, you should remove it. You should not replace the code with /Library/TeX/texbin, but instead remove the code entirely and make sure the /etc/profile file correctly executes the path_helper, which is the proper way for paths to be modified in OS X.

You can also solve this problem locally, by modifying your ~/bash_profile, to add /Library/TeX/texbin to your path, but then you will need to do this for each user on your system if you have multiple users.