this is very simplistic and only works within a line. also, i hadn't seen that you wanted the links to be in the data file, so this won't totally work. oh well.

#!/usr/bin/perl -w

use strict;

use URI::Escape;

chomp(my @words = <DATA>);

my $re_text = join '|', map quotemeta, @words;

my $re = qr/\b($re_text)\b/;

while (<>)
{
    s/$re/build_link($1)/ge;

    print;
}

sub build_link
{
    my $word = shift;

    sprintf '<A HREF="/index.pl?node=%s">%s</A>',
        uri_escape($word), $word;
}

__END__
foo
bar
baz
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