The following environment variables make sense when using Emacs:

export EDITOR="/usr/bin/emacsclient -a /usr/bin/emacs"
export ALTERNATE_EDITOR="/usr/bin/emacs"

Put it into files ~/.bashrc and ~/.xsession (and/or friends, see Environmental Settings Wiki page).

To have shell coloring in Shell Mode the following code might be helpful in ~/.bashrc.

if [ "${INSIDE_EMACS/*comint*/comint}" == "comint" -o \
     "${INSIDE_EMACS/*tramp*/tramp}" == "tramp" ] ; then
    export GIT_PAGER=""
    export TERM=ansi
fi

If you want to use sudo with Emacs Lisp function shell-command then it possibly does not work in a graphical environment like GTK+. ¹⁾ For this case i created a shell-script askpass.sh, with the following content:

#!/bin/sh
gksudo --print-pass --preserve-env --description "sudo password" 2>/dev/null

Then set environment variable

export SUDO_ASKPASS="$HOME/bin/askpass.sh"

and implement your shell command:

(shell-command (format "sudo -E -A my-sudo-cmd %s" my-sudo-execdir))