imho, it is time to get out of the PR mania and emphasize on the quality of the sites.
Have a look at those "large link directories" carefully. Are they integral part of the main site? Do the webmasters take care of the resource sites? Do they list sites of quality or list casino/inkjet printers/cheap telephones/buy viagra arbitrarily? If so, then such link directories are of little value to users and better to avoid.
If a new site with good content (useful for your visitors) approach you for a reciprocal link and you are not against reciprocal links I think it will be worth it.
Every site starts with a PR0 and a PR0 oneday can become a PR5 if you are PR-centric while building links.