Simply change the URL of submit page, for phpld, the default submission page URL is submit.php, you may edit the URL whatever you want like submit-websites.php, add-url.php, add-websites.php, etc.
phpLD 4.2 has a few different captcha choices including a newly introduced math captcha. You can also do things like setup new fields that are required in the submission. What can be great about this is it also will set your directory apart from others that only offer the typical title, url and description. You can also require people to register. You can also setup a scheduled task to clean up people who didn't pay or didn't meet some other criteria. The place spammers thrive is on directories that are just like all the others. Do yourself a favor and make something that is different.
for my own case, once i changed the url of submit page, the amount of auto bots submissions has been significantly reduced. i have not yet updated the directory software to phpld 4.2 for the math captcha, wondering whether you have plan to officially install recaptcha mod in future. i tested the mod http://www.phplinkdirectory.com/forum/showthread.php?t=21487 by Boby, installed successfully, But no idea why i don't type the recaptcha words, it can still pass to the payment page.