Creating the hash with "weights" for chapters is definitely a good idea. Now, you just have to parse each citation: 
#! /usr/bin/perl
use warnings;
use strict;
use feature qw{ say };

my %order = (
             Numbers         => 1,
             Psalm           => 2,
             Matthew         => 3,
             Luke            => 4,
             John            => 5,
             Acts            => 6,
             '2 Corinthians' => 7,
             Ephesians       => 8,
             Philippians     => 9,
             Colossians      => 10,
             Hebrews         => 11,
             '1 Peter'       => 12,
            );

sub biblically {
    my @info = map [/(.*?) ([0-9]+):([0-9]+)/], $a, $b;
    $order{$info[0][0]} <=> $order{$info[1][0]}
                        ||
            $info[0][1] <=> $info[1][1]
                        ||
            $info[0][2] <=> $info[1][2]
}

my @unsorted = split /\n/, << '__LIST__';
Acts 4:29-31
Numbers 14:10
Luke 1:20
John 16:15
Acts 2:4
1 Peter 1:22
Psalm 56:3
2 Corinthians 12:2, 4, 1, 11
Ephesians 3:18, 19
Ephesians 4:14, 13, 17, 18; 5:15, 16
Matthew 24:24
Colossians 2:6-8
Hebrews 10:35-39
Hebrews 4:10-12
Philippians 1:6, 27-29
Matthew 7:6-12, 15
Philippians 2:13-15
__LIST__

my @sorted = sort biblically @unsorted;
say for @sorted;

[download]

If the lists are very long, you might preprocess the input by so called Schwartzian transform: 

sub biblically {
    $order{$a->[0]} <=> $order{$b->[0]}
                    ||
            $a->[1] <=> $b->[1]
                    ||
            $a->[2] <=> $b->[2]
}

my @sorted = map $_->[-1],
             sort biblically
             map [/(.*?) ([0-9]+):([0-9]+)/, $_],
             @unsorted;

[download]

You didn't specify how to sort citations like

Ephesians 3:18, 19
Ephesians 3:18-21

[download]

To handle all such cases, the biblically subroutine might get even more complicated.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Regex Substring SORT Conundrum by choroba
in thread Regex Substring SORT Conundrum by Polyglot

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