my $count    = 0;
my $N        = 7;   # Example.
my $new_word = "new word";

s/(\w+)/++ $count == $N ? $new_word : $1/ge;
[download]

Untested though.

Abigail

use warnings;
use strict;

my $N = 3;
my $new = "NEW";

while (<DATA>) {
    my @words = split /\s+/;
    $words[$N-1] = $new if scalar @words >= $N;
    print join " ", @words, "\n";
}

__DATA__
hi there everyone I am looking to substitute
lots of words for new ones, but only the third
word per line on each line!
one
one two
one two three
one two three four
[download]

output:

hi there NEW I am looking to substitute 
lots of NEW for new ones, but only the third 
word per NEW on each line! 
one 
one two 
one two NEW 
one two NEW four
[download]

Just having fun with your code, however, I think this would be cool:

use warnings;
use strict;

my $N = -3;
my $new = "NEW";

while (<DATA>) {
    local $[ = 1;
    my @words = split /\s+/;
    $words[$N] = $new if @words >= abs($N);
    print join " ", @words, "\n";
}

__DATA__
hi there everyone I am looking to substitute
lots of words for new ones, but only the third
word per line on each line!
one
one two
one two three
one two three four

__END__
outputs:
hi there everyone I am NEW to substitute
lots of words for new ones, but NEW the third
word per line NEW each line!
one
one two
NEW two three
one NEW three four
[download]

Yay! Now we can specify from either end :)

Anonymously yours,
Anonymous Monk

my $n = 3;
my $newword = NEW;
my $n_minus_one = $n-1;
while (<DATA>) {
    s/((?:\w+\s+){$n_minus_one})(\w+)/$1$newword/;
    print;
}    

__DATA__
hi there everyone I am looking to substitute
lots of words for new ones, but only the third
word per line on each line!
one
one two
one two three
one two three four
__OUTPUT__
hi there NEW I am looking to substitute
lots of NEW for new ones, but only the third
word per NEW on each line!
one
one two
one two NEW
one two NEW four
[download]

s/((?:\w+\s+){$n_minus_one})(\w+)/$1$newword/;
[download]

s/((?:[\w'\-]+[^\w'\-]+){$n_minus_one})(\w+)/$1$newword/;
[download]

--

flounder