Just a couple of comments:

• use arrays instead of all those ifs -- think about the problems you'll get into if you want to add,remove or change one of alphabet sets,
• use for and foreach instead of array indexes -- they do the same thing with less code and less variables,
• when accessing a single array element use '$text[$w]' rather than '@text[$w]' -- the first character tells Perl that you want to get a scalar (single) value, not an array,
• use strict and -w (my generic advice ;-)),

And my attempt at rewriting your code:

#!/usr/bin/perl -w
use strict;

# One array instead of 2x8 if statements
my @alphabets = 
(
"seklbvrfzijdqypcnowmtxuagh",
"elbtjpwdvzqaorfiyxnukmghsc",
"velukbiyxnordctjgpwhzqafms",
"orsdvejwmcbiyhfzlukxntqgpa",
"yxsdicvejqfbhmpluaorgkztwn",
"ejqyxsdkziurgtwcaovfbhmpln",
"jqyhcaxsdlkziuevfrgtwobmpn",
"atdvnsirekmfqhwobjclgypxuz" );

my $dec = $ARGV[0] && ($ARGV[0] eq '-d'); # are we decoding?
my ( $i, $out ) = ( 0, '' );
foreach ( split / /, <STDIN> ) {          # read and split a single li
+ne
    if ( $dec ) {
        eval "tr/$alphabets[$i]/a-z/";    # decoding tr///
                                          # We need eval because tr///
+ does
                                          # not allow for substitution
+s
    } else {
        tr/A-Z/a-z/;
        eval "tr/a-z/$alphabets[$i]/";    # encoding tr/// -- as above
+, 
                                          # just reversed
    }
    $out .= "$_ ";
    $i = ($i + 1) % @alphabets;  # this will walk through 0..7 circle
}

print "$out\n";
[download]

Update: I just noticed the 'reverse' operations in your code -- I skipped them during rewrite and yet the programs are compatible ;-) 'Reverse' does not modify its argument, so you probably wanted to use @text = reverse @text;

-mk

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