Webcrawler and Excite are merging their databases and offer cross searching capabilities.
The same for Lycos, Snap and Hotbot. These are all the same company and are merging their databases.
Lycos, Excite and several others also use the DMOZ directory so if your listed there you will show up on other directories.
I personally have never used the Google, Northern Light or Magellan directories.
I agree with Matt in that you should focus your energies on a few of the major engines. The three he listed are good and I would add the open directory at dmoz.org because it is trying to catalog the internet and catch Yahoo.
After that then you should start looking for reciprocal links with other sites similar to yours.
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Thematic directories (theme oriented) are gaining in popularity due to the ongoing SPAMDEXING nonsense occuring in engines, making results irrelevant and disorganized.
Directories accept submissions by the use of humans, who have a set of rules to follow. Only pertinent sites that are professional and have related content are accepted, and categorized. Users expect better results from directories.
Open Directory Project is the backbone of several, but you must submit to each one separately. These aren't shared databases.
There's new technology being developed that will be incorporating a more directory-like style. A major part will be the quality of sites your site is linked to.
As one who, as a consultant, did research for pharmaceutical companies in engines, I can attest that the more specialized the directory, the better my results. Engines contain millions and millions of pages, many of them doorways and hallways that don't offer content. The mistake is thinking professionals follow those links. They don't.
Since so many sites don't get into Yahoo, it's important to become familiar with others.