I use cloc (cloc.sf.net) in a bash script I call 'apparently_unused'

#!/bin/bash

cloc --strip-comments=nc $1 > /dev/null 2>&1

if [ -e "$1.nc" ]
then
    subs=`grep -E "^sub " $1.nc | cut -d' ' -f2 | sort -u`
    res=();
    for sub in ${subs}
    do
        grep ${sub} $1.nc | grep -vq "sub ${sub}"
        if [ "$?" == "1" ]
        then
            res=("${res[@]}" "${sub}")
        fi
    done
    if [ ${#res[@]} == 0 ]
    then
        echo All subroutines in $1 appear to be used
    else
        echo $1 apparently unused:
        for sub in ${res[@]}
        do
            echo "  $sub"
        done
    fi
    rm $1.nc
else
    echo "failed to strip comments from $1"
fi
[download]

This is only 'apparently' unused subroutines because of calls that can be made in the way others have pointed out that this simple grep will miss. The cloc program cleans up a lot of false negatives by removing comments that may include subroutine names. Also, this assumes you have 'sub' lines that start at the first column - use perltidy.