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The main reason I have used Links is because it creates static pages for the directory as opposed to dynamic url's and rewriting short addresses.
The template system is also very easy to use and you will fairly easily be able to make it use your existing site layout.
IMHO, you are the one who would like to build a directory. It follows from this that you must have some kind of idea about what you would like this directory to do....
So, start by thinking it through: What kind of structure would you need? How should the pages look? What kind of functions would you need?
In other words: Make an exhaustive list of features first, ie your wish list.
Then, visit the directory CMS makers and start examining their systems in detail. Put checkmarks next to those of your desired features that they supply. And, if they've got a demo version try it out thoroughly so that you know if you like the way it works.
That would be one possible way to do it.
I agree with the advice about deciding on "desired features/functions" first and then looking for candidates. In some cases a very light script will do the job. In others the need is for industrial strength.
Most scripts leave some form of footprint, even where an effort is made to remove "the prints". So, by examining sites of good looking, quality, ranking directories you might get some hints. I did, at least hints worth following up on.
IYPs are local search directories, so they start with a location, then they have categories and then business listings. These contain a phone number and address and maybe a website URL and email. You can't buy scripts for these, but some scripts may superficially resemble them.
Link directories are category centric and have a URL as a minimum. The rest is optional. Scripts tend to be for this market and they seem to focus on bells and whistles rather than allow the user to customise it.
I think it is useful to describe the business model and then look for a script that comes close to this model, rather than fit the model to an available script.
For example, IYPs usually have a default ranking based on seniority within a product family, e.g. oldest Platinum customer stays #1 as long as they renew. Oldest Gold customer stays #1 below the lowest Platinum, and so on.
Some business models give each listing its own page - the business profile page (BPP). At this point you need to step back and decide how can you best optimise the type of business that will be on this page and get that page to compete for a page 1 ranking.
If you want to have a default alpha sort then how will you deal with the AAAAAAAAAArdvark kind of names that will compete for page 1 in the directory.
Will there be different price points and how will they be reflected by way of features?
You will now begin to think about textual content and it will probably go far beyond a Description field. It might include product pages.
You may want interactivity, such as maps, driving directions, iPhone app, different types of downloadable files, etc.
However.. I'm building a new directory and I haven't found a script I would like to use for it so I'm making the directory in wordpress manually. Basically I want a directory that ranks for terms and I'm not going to get that from most of the scripts out there