After taking the advice of ybiC, I've implemented Getopt::Long and Pod::UsageMan into lily.pl. I am also posting the source inline:

Updated: 3/29/03:

I rewrote about 40% of the code to be more effecient. All of the known display bugs are gone.

Updated: 4/13/03:

Lily won't die when she can't login to the POP3 server. Now you don't need to babysit the process.

#!/usr/bin/perl
#
# Lily 1.2.3 by Todd Boland <itodd@itodd.org>
# Biff was named after a dog (who barked at the mail man).
# My mail notification utility is named after my dog, Lily.

use strict;
use Tk;            # Widget set
use Net::POP3;        # To connect to POP3 server
use Getopt::Long;    # To parse the arguments
use Pod::Usage;        # For the manual

# The pop3 password is sent via command line, hide it!
$0 = "lily.pl";

# Variables used in runtime
my ($main,@frames,@buffer,%showing,$width);
my $stamp_pixmap = do { local $/; <DATA> }; 

# These variables are for buffer rotation
my ($offscreen,$lock);

# Variable needed to emulate double click
my $next;

# Variables used for controlling ticker with the mouse
my ($click,$position);

# Default optional arguments
my $opt_bg    = "#000000";
my $opt_fg    = "#00FF00";
my $opt_interval= 60;
my $opt_timeout    = 30;

# Optional arguments
my($opt_usage, $opt_manual, $opt_agent, $opt_bark, $opt_font, $opt_geo
+metry);

# Required arguments
my($arg_username, $arg_password, $arg_server);

# GetOptions parses the arguments from ARGV for me (Thanks ybiC@perlmo
+nks) :)
GetOptions(
    "usage!"    => \$opt_usage,
    "help!"        => \$opt_usage,
    "manual!"    => \$opt_manual,
    "username=s"    => \$arg_username,
    "password=s"    => \$arg_password,
    "server=s"    => \$arg_server,
    "timeout=i"    => \$opt_timeout,
    "fg=s"        => \$opt_fg,
    "bg=s"        => \$opt_bg,
    "agent=s"    => \$opt_agent,
    "bark=s"    => \$opt_bark,
    "font=s"    => \$opt_font,
    "geometry=s"    => \$opt_geometry,
    "interval=i"    => \$opt_interval,
    "width=i"    => \$width,

    # Maintain backwards compatibility
    "sound=s"    => \$opt_bark,
);

# Should we print the manual or usage?
pod2usage(-verbose => 1) and exit if(defined $opt_usage);
pod2usage(-verbose => 2) and exit if(defined $opt_manual);

# Print usage and exit if the required arguments were left out
pod2usage(-verbose => 1, -message => "Required arguments missing.") an
+d exit 
    if(!$arg_username || !$arg_password || !$arg_server);

# Convert from seconds to ms
$opt_interval = $opt_interval . ("0" x 3);

# We don't like defunct zombies
$SIG{"CHLD"} = 'IGNORE';

# Create main window
$main = new MainWindow(
    -title => "Lily",
    -bg => $opt_bg,
    -width => 640,
    -height => 35,
);

# Configure the main window
$main->overrideredirect(1);                # No decor
$main->bind("<Visibility>" => sub { $main->raise });    # Always on to
+p
$main->withdraw;                    # Initially hide it
$main->Pixmap('stamp', data => $stamp_pixmap);        # Create pixmap

# What happens when button 1 is pressed
$main->bind("<ButtonPress-1>" => sub {
    $position = $main->pointerx - $main->x;
    $click = 1;
});

# What happens when button 1 is released
$main->bind("<ButtonRelease-1>" => sub {
    $click = 0;
});

# What happens when the mouse moves inside the window
$main->bind("<Motion>" => sub {
    if($click) {
        &move_ticker($main->pointerx - $main->x - $position);
        $position = $main->pointerx - $main->x;
    }
});

# Update the main window
$main->update;

# Resize if geometry specified
$main->geometry($opt_geometry) if($opt_geometry);

# Check mail timer
$main->repeat($opt_interval, sub {
    &check_mail;
});

# We need an initial call to check the mail upon starting
&check_mail;

# Move the ticker
$main->repeat(20, sub {
    return if $click or !defined $frames[0];
    &move_ticker(-1);
});

# Main program loop
MainLoop;

# Routine to rotate messages in the buffer to the display
sub rotate_buffer {

    my($offscreen,$headers) = @_;
    my($new_from,$new_subject) = @{$headers};

    # Fetch old headers
    my($stamp,$label) = $frames[$offscreen]->children;
    my($old_subject,$old_from) = 
        split(/\n/, $label->cget("-text"));

    # Put new headers into the label
    $label->configure(
        -text => "$new_subject\n$new_from"
    );

    [$old_from, $old_subject];
}

# Routine to move the entire ticker
sub move_ticker {
    my $movement = shift;

    # This prevents underrun
    return if defined $lock;
    $lock = 1;

    # To the right?
    if($movement > 0) {
        if($frames[0]->x + $movement > $main->width) {
        
            # Move the left side
            $frames[0]->place(-x => $frames[0]->x - ($main->width + $f
+rames[0]->width) + $movement);

            # Ratate if there are messages in the buffer
            push(@buffer, &rotate_buffer(0, shift @buffer))
                if $#buffer >= 0;
        } else {
        
            # Move along
            $frames[0]->place(-x => $frames[0]->x + $movement);
        }
    
    # To the left?
    } elsif($movement < 0) {
        if($frames[0]->x + $frames[0]->width < 0) {

            # Move to right side
            $frames[0]->place(-x => $frames[0]->x + $frames[0]->width 
++ $main->width + $movement);

            # Rotate if there are messages in the buffer
            unshift(@buffer, &rotate_buffer(0, pop @buffer))
                if $#buffer >= 0; 
        } else {

            # Move along
            $frames[0]->place(-x => $frames[0]->x + $movement);
        }
    }

    # Update the first frame so we can get the new x coords
    $frames[0]->update;
    my $new_x = $frames[0]->x + $width;

    # Every frame should follow 256 pixels apart
    for(my $i=1; $i<=$#frames; $i++) {

        # Figure new x for frame
        $new_x = $new_x - $main->width - $width 
            if($new_x >= $main->width);

        # Should we rotate the buffer?
        if($#buffer >= 0) {
            if($frames[$i]->x > 0 && $new_x < 0 && $movement > 0) { 
                push @buffer, 
                    &rotate_buffer($i, shift @buffer);

            } elsif($frames[$i]->x < 0 && $new_x > 0 && 
                $movement < 0) {
                unshift @buffer, 
                    &rotate_buffer($i, pop @buffer);
            }
        }

        # Place frame, get new x coord and update
        $frames[$i]->place(-x => $new_x);
        $new_x += $width;
        $frames[$i]->update;
    }

    # unlock the routine
    $lock = undef;
}

# The routine that checks for new mail
sub check_mail {
    my($new_messages, $bark);

    # Login to POP3 server
    my $pop = new Net::POP3(
        $arg_server, 
        timeout => $opt_timeout,
    ) or do {
        warn "Invalid POP3 server.";
        return;
    };

    # Count the number of messages waiting
    $new_messages = $pop->login($arg_username, $arg_password) or do {
        warn "POP3 login failed.";
        return;
    };

    # List messages
    for(my $i=1; $i<=$new_messages; $i++) {
        my($from,$subject,$id);

        # Fetch headers
        foreach my $header ($pop->top($i)) {
            foreach(@{$header}) {

                # Net::POP3 doesnt chomp for us
                chomp;
                
                # Only snag the first 43 chars to keep em short
                $from    = substr($_,0,43) if(/^(From):\s+/i);
                $subject= substr($_,0,43) if(/^(Subject):\s+/i);
                $id = $1 if(/^Message-Id:\s*(.*)$/i);
            }
        }

        # Add ... if string is longer than the allowed length
        $subject = substr($subject,0,40) . "..." if(length($subject) >
+ 40);
        $from = substr($from,0,40) . "..." if(length($from) > 40);

        # Unless the item is already showing
        unless($showing{$id}) {
        
            # Don't show it again!
            $showing{$id} = 1;

            # Did it fit?
            if(&add_frame($from, $subject) == -1) {

                # No, put it in the buffer
                unshift @buffer, [$from, $subject];
            }

            # Toggle barking
            $bark = 1;
        }
    }

    # Close pop connection
    $pop->quit();

    # Bark?
    if($opt_bark && $bark) {
        my $pid = fork;
        if($pid == 0) {
                    
            # Die after barking
            exec($opt_bark);
            exit;
        }
    }
}

# Routine to add message to display
sub add_frame {
    my($from,$subject) = @_;
    my($x,$stamp,$label);

    # Bring up main window
    $main->deiconify;
    $main->raise;

    # Where oh where shall we put it?
    $x = ($#frames >= 0) ? $width * ($#frames + 1) : 0;

    # Put it in the buffer
    return -1 if($x >= $main->width + $width); 

    # Create frame
    push @frames, $main->Frame(
        -height => $main->height,
        -bg => $opt_bg,
    )->place(-x => $x);

    # Create Stamp
    $stamp = $frames[$#frames]->Label(
        -image => 'stamp',
        -bg => $opt_bg,
    )->place(-x=>0,-y=>0);

    # Configure stamp
    $stamp->bind("<ButtonRelease-1>" => \&release ) if($opt_agent);
    $stamp->configure( -cursor => "hand2") if ($opt_agent);

    # Create label
    $label = $frames[$#frames]->Label(
        -justify => "left",
        -text => "$subject\n$from",
        -fg => $opt_fg,
        -bg => $opt_bg,
        -width => 38,
        -anchor => "w",
    )->place(-x=>0,-y=>0);

    # Configure label
    $label->configure( -font=> $opt_font) if($opt_font);
    $label->bind("<ButtonRelease-1>" => \&release ) if($opt_agent);
    $label->configure( -cursor => "hand2") if ($opt_agent);

    # Re-configure the frame
    $frames[$#frames]->update;
    $width = $label->width + $stamp->width if !defined $width;
    $frames[$#frames]->configure(-width=>$width);
    $frames[$#frames]->update;

    # Place label
    $label->place(
        -x => $stamp->width,
        -y => $frames[$#frames]->height / 2 - $label->height / 2,
    );

    # Place stamp
    $stamp->place(
        -x => 0,
        -y => $frames[$#frames]->height / 2 - $stamp->height / 2,
    );
}

# Mouse release routine
sub release {

    # Cancel any moves
    $click = 0;

    # Emulate a double click since Double-ButtonPress 
    # doesn't work on moving labels
    if(!$next) {
    
        # Double click rate is 250ms
        $main->after(250, sub {
            $next = 0;
        });
        $next = 1;

        # It's only the first click, return
        return;
    }
    $next = 0;

    # Destroy the active frames
    while(my $frame = pop @frames) {
        my @children = $frame->children;
        foreach(@children) {
            $_->destroy();
        }
        $frame->destroy();
    }

    # Return buffer and frames arays to their defaults
    undef @buffer;
    undef @frames;

    # Launch email client?
    if($opt_agent) {
        my $pid = fork;
        if($pid == 0) {

            # Launch the  mail client
            exec($opt_agent);
            exit;
        }
        $main->withdraw;
    }
}

# The pod
=head1 NAME

lily.pl

=head1 SYNOPSIS

lily.pl [-option=VALUE ...] B<-username=USERNAME -password=PASSWORD -s
+erver=SERVER>

=head1 DESCRIPTION

Scrolls From: and Subject: headers of all email found on SERVER using 
+USERNAME 
and PASSWORD as the login information.

=head1 ARGUMENTS

=item B<-server=SERVER>        Use SERVER as the POP3 server

=item B<-username=USERNAME>    Use USERNAME for username on SERVER

=item B<-password=PASSWORD>    Use PASSWORD for password on SERVER

=head1 OPTIONS

=item -timeout=SECONDS    Timeout after SECONDS seconds

=item -fg=COLOR            Use COLOR for the foreground

=item -bg=COLOR            Use COLOR for the background

=item -agent=COMMAND        Execute COMMAND to launch mail agent

=item -bark=COMMAND        Execute COMMAND on new mail

=item -font=FONT        Use FONT to display headers

=item -width=PIXELS        Make each message PIXELS pixels wide

=item -geometry=GEOMETRY    Use GEOMETRY to map window

=item -interval=SECONDS    Check mail every SECONDS seconds

=item -manual            Display the manual

=item -usage            Show usage screen

=head1 EXAMPLE

This is my configuration:

lily.pl -bark="plaympeg /home/itodd/newmail.mp3" -agent="mozilla -remo
+te xfeDoCommand\(openInbox\) || mozilla -mail" -interval=30 -font="-*
+-helvetica-medium-r-*-*-10-*-*-*-*-*-*-*" -geometry="1280x30+0-0" -wi
+dth=256 B<-username=USERNAME -password=PASSWORD -server=SERVER>

=head1 AUTHOR

Todd Boland <itodd@itodd.org> http://www.itodd.org

=cut

# The stamp xpm
__DATA__
/* XPM */
static char * stamp_xpm[] = {
"16 16 3 1",
"     c None",
"#    c #FFFFFF",
"%    c #0000FF",
"                ",
" ##  ##  ##  ## ",
" ############## ",
"  #%%%%%%%%%%#  ",
"  #%%%%##%%%%#  ",
" ##%%%####%%%## ",
" ##%%######%%## ",
"  #%%%%##%%%%#  ",
"  #%%%%##%%%%#  ",
" ##%%%%##%%%%## ",
" ##%%%%##%%%%## ",
"  #%%%%%%%%%%#  ",
"  #%%%%%%%%%%#  ",
" ############## ",
" ##  ##  ##  ## ",
"                "};
[download]