Number one, get in the habit of using -w, and use strict;.

Try it this way. Others will add more changes.

#!/usr/bin/perl -w 
# untitled1.pl 
use strict;

open(shortcuts,"location.txt" || die"Can't open the stinkin' file"); 
@file = ; 
close(shortcuts); 
foreach $line (@file) { 
# The chomp isn't necessary. And you don't need the backticks.
  system($line);
}

location.txt 
c:/program files/netscape/communicator/program/netscape.exe 
c:/Program Files/Netscape/Communicator/Winamp/winamp.exe 
c:/Program Files/Netscape/Communicator/Program/AIM/aim.exe
[download]

- Ozymandias