These are the top directories that accept free submissions. All of these directories will help improve your link popularity and will aid in getting your site spidered by the major search engines.
About.com
About.com is a searchable directory of topical guides, each run by an expert for each topic. Submissions are free, but not all sites are included. About.com stresses quality over quantity. To be considered for a listing, find the category that is most relevant to your site. Then, send an email message to the guide requesting that you be included.
Open Directory Project
Volunteer build and maintained directory. Extremely important for search engine marketers because Google uses it for its directory. To submit your site, you will need to find the most appropriate category. Don't try and submit to a top level category, drill down through the general categories to find the most specific category you can for your site. Before submitting, it is a good idea to review the guidelines.
Gimpsy
An Internet directory that only holds carefully reviewed interactive sites, using a unique action based classification method. Free site submission. Be sure and review their submission guidelines.
GoGuides.Org
A volunteer run and edited directory. You will need to find the most appropriate category for listing your site and then look for the "Add URL" link. This will lead you to a page with two options for submission - one free, one paid. For free submissions, you'll have to become a "Guide." Anyone can become a Guide and you won't be required to submit any more sites if you don't want to. Submission guidelines.
JoeAnt.com
Search, find and dig exactly what you're looking for by subject or boolean. JoeAnt.com is about providing a directory of quality sites for Internet users. Our goal is to list the best sites for a wide variety of topics giving our users the most relevant results for their searches. To submit your site, drill down to the most appropriate category and find the "Become an Editor" link. You have to be an editor to submit to JoeAnt.com, but anyone can become one and you are required to submit any more sites if you don't want to. Submission guidelines.
Skaffe.com
Searchable human edited international directory with family safe viewing filtered for spam and adult content. Find the category that best suits your site and look for the submit link.
Web-Beacon
Web-Beacon is a virtual community made up of people from all over the world brought together by common goals: to build and maintain a directory of the highest quality and give each and every member a voice in its growth and operation.
WebSavvy
Submit your site to the proper category by first selecting a category in the Main Category selection menu. The Subcategory selection menu's will self-populate, allowing you to narrow it down to the most suitable category selection for submission of your site. Submission Guidelines.
WoW Search Engine and Directory Service
World, local and regional search engine and directory featuring one of the webs most comprehensive topic structures and free submission.
Free only for non-commercial sites:
Yahoo!
Yahoo! now charges for all commercial submissions to their directory. But, if your site is not commercial and you don't mind waiting months to be included, you can still submit your site for free. Just drill down to the most appropriate category and look for the "Suggest a Site" link.
Zeal
Web directory and search engine built by the knowledge and experience of Internet enthusiasts like you. Find ratings, reviews, and the best websites. Like Yahoo!, Zeal only accepts free submissions for non-commercial sites. To submit a site, you are required to go through registration.