I'm afraid this doesn't appear to work on anything with comments... For example, try running it on this script:

print "Foo.\n";
$foo='bar'; # This is a comment
print "No, $foo.\n"; # Another comment.
[download]

...and it will go something like this:

C:\test\scratch>copy con obs.pl
#!/usr/local/bin/perl
$input = $ARGV[0];
open(thefile,"$input");
@file = <thefile>;
close thefile;
open(newfile,">$input");
$counter = 0;
foreach $line(@file)
{
        $counter++;
        if ($counter != 1)
        {
                $line =~ s/\s+$//;
                $line =~ s/^\s+//;
        }
        print newfile "$line";
}
close newfile;
^Z
        1 file(s) copied.

C:\test\scratch>copy con test2.pl
print "Foo.\n";
$foo='bar'; # This is a comment
print "No, $foo.\n"; # Another comment.
^Z
        1 file(s) copied.

C:\test\scratch>test2.pl
Foo.
No, bar.

C:\test\scratch>obs test2.pl

C:\test\scratch>type test2.pl
print "Foo.\n";
$foo='bar'; # This is a commentprint "No, $foo.\n"; # Another comment.

C:\test\scratch>test2.pl
Foo.
[download]

oh yeah, never tested that, I dont use comments, bad habit, I know, but it makes it harder for me to read perl code if comments are in there.

I love the way you print to a file named input.