Perl has a sort built in to do things like this. You will also want to checkout split. Depending on how the files are set up (delimiter) you are going to want to split on that and sort by the correct element. An example (untested) for something like this would be the following. We are splitting on commas.

 
#!/usr/bin/perl -w 
use strict;   #always use strict

my %sortKey;

open (INFILE, "filename");   #open the file
while <INFILE> { #iterate through the file line by line
   my @tmp = split /,/;   #split the file on the comma
   
   #for the sake of the example we will say that the first 
   #element of the file is what you want to sort on
   #so we will make it the key to our hash
   $sortKey{$tmp[0]}=$_;
}

open (OUTFILE ">outfile");

#this will take the keys, shove them in an array, sort 
#them and set $key equal to the current sorted key
foreach my $key (sort(keys(%sortKey))) {
   print OUTFILE " %sortKey{$key};
}
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Hopefully this will give you a pretty good idea how to do the first part, and enough info on how to do the second part. Feel free to /msg me if you have questions.
UPDATE: fixed a syntax error