First a few things that are nothing to do with your immediate problem, but do relate to your "sloppy code" comment:

First, always use strictures (use strict; use warnings;) Warnings (the -w switch on the "command line") are good, but strict is much better because to performs what amounts to a static analysis of your code to alert you to common errors like mismatched variable names.

Don't use subroutine prototypes (sub proto () { the () makes it a prototype). They don't do what you think and will bite you on the bum!

Don't overuse the default variable ($_). It gets clobbered all over the place so is a great source of bugs and using it doesn't help understand the code - a named lexical variable (one declared with my) is much better on both counts.

It's great to see you using three parameter open and checking the result. It would be even better if you used a lixical file handle (one declared with my) and in your error message said which file failed to open.

Ok, now to address your real problem. First off what you have commented out would only be a one shot test because by the end of the loop the file handle is stuck at the end of the file. You'd have to reset the file handle, or re-open the file to fix that. However rereading a file multiple times is bad design. Much better to read the data once into a data structure you can look up in memory. Consider:

#!/usr/local/bin/perl
use strict;
use warnings;

my $kSkipSeconds = 3600;
my %epochs;

while (<DATA>) {
    chomp;
    
    my ($ip, $epoch) = split /,/;
    
    next if ! $epoch;
    $epochs{$ip} = $epoch;
}

my @ip_array = qw(1.1.1.1 1.1.1.3 1.1.1.2);
my $now = 1320640620; # time()

for my $ip (@ip_array) {
    if (exists $epochs{$ip} && $epochs{$ip} + $kSkipSeconds > $now) {
        print "Skipping $ip\n";
        next
    }
    
    print "Time to update $ip\n";
    $epochs{$ip} = $now;
}

print "------------ updated epochs -------------\n";
print "$_,$epochs{$_}\n" for sort keys %epochs;


__DATA__
1.1.1.1,1320639902
1.1.1.3,1320640560
1.1.1.2,1320600900
[download]

Prints:

Skipping 1.1.1.1
Skipping 1.1.1.3
Time to update 1.1.1.2
------------ updated epochs -------------
1.1.1.1,1320639902
1.1.1.2,1320640620
1.1.1.3,1320640560
[download]

Well I thought I had some stuff figured out and after another 15 hours of reading/testing I haven't gotten much further.

I thought the ping part was working but now it seems intermittent, and I still can not get the foreach part to work. Basically I do not want to email a failure notive about the same failed ping to a host/IP until some time has passed, maybe 2-3 failures or something. While trying to ping once every 5 minutes. I have tried literally dozens of different ways to skip over the IP if it is on the email.list -- unless ($_ =~ my @eFile) -- was my last attempt but I can't get anything to work there.

Any assistance is appreciated, thanks Sam.

#!/usr/local/bin/perl
use strict;
use warnings;
use Net::Ping;
use Net::SMTP;

my $from = 'from@email.com';
my $site = 'email.com';
my $smtp_host = 'smtp.email.com';
my $to = 'to@email.com';
my $smtp = Net::SMTP->new($smtp_host, Hello => $site);


my $oFile = open(oFILE, ">", "output.file") or die("unable to write to
+ $!\n");

my $hFile = open(hFILE, "<", "host.file") or die("unable to open $!\n"
+);
my @ip_array = <hFILE>;
chomp(@ip_array);

my $eFile = open(eFILE, ">", "email.file") or die("unable to write to 
+$!\n");
my @efile = <eFILE>;
chomp(@efile);

sub email {    
    $smtp->mail($from);
    $smtp->to($to);
    $smtp->data();
    $smtp->datasend("To: $to\n");
    $smtp->datasend("Subject: Ping failure notice.\n");
    $smtp->datasend("\n");
    $smtp->datasend("Ping failed on host $_\n");
    $smtp->dataend;
    print eFILE ("$_\n");
}

my $p = Net::Ping->new();

foreach (@ip_array) {
        if($p->ping($_)) {
            print oFILE ("$_ is responding to ping.\n");
        } else {
            print oFILE ("$_ is NOT responding to ping.\n");
            unless ($_ =~ my @eFile) {
            email();
            }
        }    
        }

close(hFILE);
close(oFILE);
close(eFILE);

$p->close();
$smtp->quit;

#End of Code
[download]

The files I am using:

--host.file--
www.cnn.com
127.0.0.1
10.10.10.1
178.23.1.2
9.1.1.1>

--email.file--
<empty>

--output.file--
<empty>
[download]