What advice do you have to make directories stand out as something more than just a listing of websites like all the other directories out there? Have you tried adding a blog or forum to make your directory different from all the others?
If you add a blog or forum it's not a pure directory site any more, in my opinion. It becomes more of a portal. One approach is to add extra information to your listings, other than the standard. Some directories have ratings and "cool" awards. Others have longer site descriptions. Some offer keyword searching, some don't. I think the most important way to differentiate what you offer is in the sites you accept and reject, and how you categorise them. Do you want to build a comprehensive directory that includes most sites, or an exclusive one that only showcases the best sites you can find? And is your category structure well-thought-out and easy to navigate?
I've only seen a couple directories doing this, so far, but a good thing to do, as far as unique content goes, is to place a descriptive paragraph or two at the top of each category and sub-category. This way google bot gets to chew on some actual real content, not just the same script generated category titles, and then a bunch of links and descriptions its seen over and over again in other directories. Might pull a bit more search traffic to the directory, and give the directory a tad bit more value, in SE's eyes, thus giving submitted links more value to. Maybe. As we all know, phpld sites are becoming a dime a dozen, and anything that would make your directory unique, from a spiders point of view, will make your directory more valuable.
I do that at the top of my main categories. I think it helps visitors know what to expect, because a single-word category title doesn't tell you an awful lot. I find that, visiting other directories, some people have completely different ideas about what should be listed under Arts, Entertainment, or even Travel, for instance.
How about a mod or add on that allows visitors to comment, review, and rate on websites in your directory? Do any of the popular scripts like phpld have such a thing?
I've certainly seen directories that allow users to leave a rating, so it's probably a commonly available mod. I don't know about leaving comments, though. The only problem is, such a thing sucks. It's one thing to allow your editors to decide which sites are "cool" and top-rated resources, because for the majority of sites they will be able to give an objective view. But user ratings are widely abused, and IMHO worthless. You just get too many webmasters trying to boost their own sites, so the feature has no value at all to the casual searcher.