Hi Deep Plaid,

.. I know a hash won't work because I will have rows of data with "keys" that are duplicated, and that have multiple values..
Really? Except I don't understand what you wanted. Am sure, hash would work perfectly, using the dataset you presented like so:

use warnings;
use strict;

use Data::Dumper;

my $file = "1.00 InDev 01-Jun-2013
1.00 InTest 15-Jul-2013
1.00 InUAT 31-Jul-2013
1.00 InProd 15-Sep-2013
1.01 InDev 01-Jul-2013
2.00 InDev 01-Aug-2013
3.00 InDev 01-Sep-2013";

my %line;
for ( split /\n/, $file ) {
    my @datas = split;
    push @{ $line{ $datas[0] }{ $datas[1] } }, $datas[2];
}
{
$Data::Dumper::Sortkeys = 1;
$Data::Dumper::Indent = 3;
print Dumper \%line;
}
[download]

Which gives the following output:

$VAR1 = {
          '1.00' => {
                      'InDev' => [
                                   #0
                                   '01-Jun-2013'
                                 ],
                      'InProd' => [
                                    #0
                                    '15-Sep-2013'
                                  ],
                      'InTest' => [
                                    #0
                                    '15-Jul-2013'
                                  ],
                      'InUAT' => [
                                   #0
                                   '31-Jul-2013'
                                 ]
                    },
          '1.01' => {
                      'InDev' => [
                                   #0
                                   '01-Jul-2013'
                                 ]
                    },
          '2.00' => {
                      'InDev' => [
                                   #0
                                   '01-Aug-2013'
                                 ]
                    },
          '3.00' => {
                      'InDev' => [
                                   #0
                                   '01-Sep-2013'
                                 ]
                    }
        };
[download]

So, one out of your questions, is actually done for you, the second one you can easily do. :)!
^*I hope the above helps. You can also take a look at perldsc

* Update