I use URI:

#!/usr/bin/perl

use strict;
use warnings;

use URI;
my $base_uri = URI->new( '/home/httpd/project/' );

while (my $path = <DATA>) {
  chomp($path);
  my $absolute = URI->new_abs( $path, $base_uri );
  printf "%s + %s: %s\n", $base_uri->canonical, $path, $absolute->cano
+nical;
}

__DATA__
../another/
subdir/
../../../etc/very/dangerous
../project/
[download]

update: it seems that I didn't understand the question, sorry.
update2: However, it seems that URI::file does understand OS differences and does what you want:

use URI::file;
my $base_uri = URI::file->new( URI::file->cwd );

while (my $path = <DATA>) {
  chomp($path);
  my $absolute = URI::file->new_abs( $path, $base_uri );
  printf "%s + %s: %s\n", $base_uri->canonical, $path, $absolute->file
+;
}

__DATA__
../another/
subdir/
../../../some/other/place
../project/
[download]