Other than that I'd rather quit my job than have to maintain code written like that, I have one comment. The following:

unless ($G)
{
 if (!($P) && $shifted =~ /\w/)
 {
   @files = split /,/, $shifted;
   foreach (@files)
   {
     warn "You asked me to eat \"$_\" and I\'m going to taste it and s
+ee if its real.\n" if $D;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   $!\n   (...because of this error, i'm going to stop)\n
+" unless -e $_;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   It\'s a directory, not a file.\n   (try this):\n\nls $
+_ | perl -pe \'s/^/$0 $_\\//;' > shx && sh -x shx\n\n" if -d $_;
     warn "Yep, tastes like a file.\n" if $D;
     eat($_);
   }
 }
 elsif ($P)
 {
   smoke();
 }
 elsif ($s)
 {
   subliminal_meaning($s);
 }
 elsif ($m)
 {
   individual_meaning($m);
 }
 else
 {
   die "$usage";
 }
}
else
{
 if (!($P) && $shifted =~ /\w/)
 {
   @files = split /,/, $shifted;
   foreach (@files)
   {
     warn "You asked me to eat \"$_\" and I\'m going to taste it and s
+ee if its real.\n" if $D;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   $!\n   (...because of this error, i'm going to stop)\n
+" unless -e $_;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   It\'s a directory, not a file.\n   (try this):\n\nls $
+_ | perl -pe \'s/^/$0 $_\\//;' > shx && sh -x shx\n\n" if -d $_;
     warn "Yep, tastes like a file.\n" if $D;
     imagine($_);
   }
 }
 elsif ($P)
 {
   plumbing();
 }
 elsif ($s)
 {
   subliminal_meaning($s);
 }
 elsif ($m)
 {
   individual_meaning($m);
 }
 else
 {
   die "$usage";
 }
}
[download]

would be better written as

 if (!($P) && $shifted =~ /\w/)
 {
   @files = split /,/, $shifted;
   foreach (@files)
   {
     warn "You asked me to eat \"$_\" and I\'m going to taste it and s
+ee if its real.\n" if $D;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   $!\n   (...because of this error, i'm going to stop)\n
+" unless -e $_;
     die "You fed me \"$_\" and I couldnt find it or couldnt touch it 
+because...\n   It\'s a directory, not a file.\n   (try this):\n\nls $
+_ | perl -pe \'s/^/$0 $_\\//;' > shx && sh -x shx\n\n" if -d $_;
     warn "Yep, tastes like a file.\n" if $D;
     if ($G) { imagine($_); } else { eat($_); }
   }
 }
 elsif ($P)
 {
   if ($G) { plumbing(); } else { smoke(); }
 }
 elsif ($s)
 {
   subliminal_meaning($s);
 }
 elsif ($m)
 {
   individual_meaning($m);
 }
 else
 {
   die "$usage";
 }
[download]

Similarly,

foreach(sort keys %switches) {
  ${$_}= "$switches{$_}";
  print " * \$$_ is switched \"$switches{$_}\"" if $D;

  if ($switches{$_} eq '1') { print " (ON)" if $D;  }
  if ($switches{$_} eq '0') { print " (OFF)" if $D; }
  print "\n" if $D;
}
[download]

is probably better written as

foreach(sort keys %switches) {
  ${$_}= "$switches{$_}";
  if ($D) {
    print " * \$$_ is switched \"$switches{$_}\"";

    if ($switches{$_} eq '1') { print " (ON)"; }
    if ($switches{$_} eq '0') { print " (OFF)"; }
    print "\n";
  }
}
[download]

Also, in...

  $G ?
    ( $extra = " ***GAPS***" )
    :
    ( $extra = " >>>SIGNALS<<<" );
    
  $S ? 
    ( $H ? print "WIDTH\tCOUNT\tSPOON$extra\n" : 0 )
    :
    ( $H ? print "WIDTH\tCOUNT$extra\n" : 0 );
[download]

you seem to be missing the point of the trinary operator. Yes you could use it like a shorthand 'if', but its job is to select between to choices of data rather than code. I wouldn't mention it except you've got a textbook case for its usage here!

  $extra = 
    $G
      ? " ***GAPS***"
      : " >>>SIGNALS<<<";
  
  $H and print 
    $S
      ? "WIDTH\tCOUNT\tSPOON$extra\n")
      : "WIDTH\tCOUNT$extra\n";
[download]

Based on that, I'm wondering if you've got a bug (a missing print) here:

    $S ? "$_\t$seen{$_}{count}\t$seen{$_}{spoon}\n" : print "$_\t$seen
+{$_}{count}\n";
[download]

I also think you've got way too much useless use of quotes (e.g. "$usage"), and unnecessary backwhacking of quotes.