And, as always, make sure that you give a complete path to your system commands (e.g. lynx) so the CGI script knows where it is. I recommend putting them all at the top of your script for easy maintenance:

#!/bin/perl -- major peices missing, but you get the picture

use CGI;

my $lynx = "/usr/bin/foo/bar/lynx";
my $wget = "/export/home/genghis/bin/wget";

##etc..
[download]

Same goes for that ourput file in your example (file.txt) - make sure you are giving an absolute path, as you cannot be sure from what directory lynx is being invoked.

Heck, as a general rule of thumb, use absolute paths for everything - it will save a lot of trouble in the long run. :)