Japhy hit the nail on the head, so let me just offer some stylistic suggestions for that first script:

#...
my $Usage = "Usage: $0 {-b|-h} input.file output.file\n";

my ( $outType, $inpFile, $outFile ) = @ARGV;

open (INP,"<$inpFile") || die "Can't read $inpFile: $!";
open (OUT,">$outFile") || die "Can't write $outFile: $!";

if ($outType =~ /^-h$/i) {
    binhex();
}
elsif ($outType =~ /^-b/i) {
    hexbin();
}
else {
    die $Usage;
}
#...
[download]

If you decide to add more options later, you should look into GetOpt::Std or GetOpt::Long.