If you have more than 30 Repositories, the original script will not download all. The github api limits the entries to 30 per page but you can raise that up to 100. I have added a small loop which sets the limit to 90 and cycles through all pages until the listing on a page is empty...

backup-github.sh

#!/bin/bash 
# A simple script to backup an organization's GitHub repositories.

GHBU_BACKUP_DIR=${GHBU_BACKUP_DIR-"github-backups"}                  # where to place the backup files
GHBU_ORG=${GHBU_ORG-"<CHANGE-ME>"}                                   # the GitHub organization whose repos will be backed up
GHBU_UNAME=${GHBU_UNAME-"<CHANGE-ME>"}                               # the username of a GitHub account (to use with the GitHub API)
GHBU_PASSWD=${GHBU_PASSWD-"<CHANGE-ME>"}                             # the password for that account 
GHBU_GITHOST=${GHBU_GITHOST-"<CHANGE-ME>.github.com"}                # the GitHub hostname (see notes)
GHBU_PRUNE_OLD=${GHBU_PRUNE_OLD-true}                                # when `true`, old backups will be deleted
GHBU_PRUNE_AFTER_N_DAYS=${GHBU_PRUNE_AFTER_N_DAYS-3}                 # the min age (in days) of backup files to delete
GHBU_SILENT=${GHBU_SILENT-false}                                     # when `true`, only show error messages 
GHBU_API=${GHBU_API-"https://api.github.com"}                        # base URI for the GitHub API
GHBU_GIT_CLONE_CMD="git clone --quiet --mirror git@${GHBU_GITHOST}:" # base command to use to clone GitHub repos

TSTAMP=`date "+%Y%m%d-%H%M"`

# The function `check` will exit the script if the given command fails.
function check {
  "$@"
  status=$?
  if [ $status -ne 0 ]; then
    echo "ERROR: Encountered error (${status}) while running the following:" >&2
    echo "           $@"  >&2
    echo "       (at line ${BASH_LINENO[0]} of file $0.)"  >&2
    echo "       Aborting." >&2
    exit $status
  fi
}

# The function `tgz` will create a gzipped tar archive of the specified file ($1) and then remove the original
# the option -P omits the error message tar: Removing leading '/' from member names
function tgz {
   check tar zcPf $1.tar.gz $1 && check rm -rf $1
}

$GHBU_SILENT || (echo "" && echo "=== INITIALIZING ===" && echo "")

$GHBU_SILENT || echo "Using backup directory $GHBU_BACKUP_DIR"
check mkdir -p $GHBU_BACKUP_DIR

$GHBU_SILENT || echo "Fetching list of repositories for ${GHBU_ORG}..."
# cycling through pages as github API limits entries to 30/100 per page...
PAGE=0
while true; do
  let PAGE++
  $GHBU_SILENT || echo "getting page ${PAGE}"
  REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | grep "\"name\"" | awk -F': "' '{print $2}' | sed -e 's/",//g'`
  if [ -z "${REPOLIST_TMP}" ]; then break; fi
  REPOLIST="${REPOLIST} ${REPOLIST_TMP}"
done


$GHBU_SILENT || echo "found `echo $REPOLIST | wc -w` repositories."


$GHBU_SILENT || (echo "" && echo "=== BACKING UP ===" && echo "")

for REPO in $REPOLIST; do
   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO}"
   check ${GHBU_GIT_CLONE_CMD}${GHBU_ORG}/${REPO}.git ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}-${TSTAMP}.git && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}-${TSTAMP}.git

   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO}.wiki (if any)"
   ${GHBU_GIT_CLONE_CMD}${GHBU_ORG}/${REPO}.wiki.git ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.wiki-${TSTAMP}.git 2>/dev/null && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.wiki-${TSTAMP}.git

   $GHBU_SILENT || echo "Backing up ${GHBU_ORG}/${REPO} issues"
   check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/repos/${GHBU_ORG}/${REPO}/issues -q > ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.issues-${TSTAMP} && tgz ${GHBU_BACKUP_DIR}/${GHBU_ORG}-${REPO}.issues-${TSTAMP}
done

if $GHBU_PRUNE_OLD; then
  $GHBU_SILENT || (echo "" && echo "=== PRUNING ===" && echo "")
  $GHBU_SILENT || echo "Pruning backup files ${GHBU_PRUNE_AFTER_N_DAYS} days old or older."
  $GHBU_SILENT || echo "Found `find $GHBU_BACKUP_DIR -name '*.tar.gz' -mtime +$GHBU_PRUNE_AFTER_N_DAYS | wc -l` files to prune."
  find $GHBU_BACKUP_DIR -name '*.tar.gz' -mtime +$GHBU_PRUNE_AFTER_N_DAYS -exec rm -fv {} > /dev/null \; 
fi

$GHBU_SILENT || (echo "" && echo "=== DONE ===" && echo "")
$GHBU_SILENT || (echo "GitHub backup completed." && echo "")
ACT  SAVE  READ  SHARE  FOLLOW  

Just a note for everyone - there have been recent API changes (an addition of a license object that blows up the script.)

Change

REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | grep "\"name\"" | awk -F': "' '{print $2}' | sed -e 's/",//g'`

to

REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | ./processRepoList`

and add the python script

#! /usr/bin/env python2

# Takes a JSON file (a list of objects) and pulls out only the 'name' key/value pair of each object - printing out the value

import json
import sys

data = json.load(sys.stdin)
for x in data:
	print x['name']

I've added one change to adjust to new changes. Because when License information is added, the backup does not work fine.

`REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | grep "\"name\"" | awk -F': "' '{print $2}' | sed -e 's/",//g'``

Should change to:

#REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | grep "\"name\"" | awk -F': "' '{print $2}' | sed -e 's/",//g'`
 REPOLIST_TMP=`check curl --silent -u $GHBU_UNAME:$GHBU_PASSWD ${GHBU_API}/orgs/${GHBU_ORG}/repos\?page=${PAGE}\&per_page=90 -q -k | grep "\"full_name\"" | cut -d'/' -f2 | sed -e 's/",//g'`