There are a few reasons to submit your website to link directories. The first reason
is to create more traffic and exposure to your website. To take the most advantage of this, you will need to look for directories that are related to your website, or have categories related to your website. You will also need to look for directories that have a lot of traffic themselves. If you can submit your website and can choose the title of the website (the link text), make sure you put a desired keyword phrase in the title, for example you may want to title your website "business ecommerce solutions for small businesses". This will give you some keyword ranking in the search engines if the links don't have a nofollow tag.

This brings us to the other reason to submit your website to link directories, link popularity. This only works if the link directories don't have nofollow tags. If the directories have nofollow tags (you can see this by looking at the source code), then unless the directories get a lot of traffic (look at it's Alexa ranking), it probably won't be worth your time to submit your website.

Below, is a list of some higher page rank directories. Some of them cost to submit your website to them:

dmoz (open directory project)
Yahoo! Directory
Librarians' Internet Index
Inc.com
Nature.com
About.com
BBBOnLine
Business.com
Uncover the Net
Best of the Web
JoeAnt.com
eHub
FreeIndex
Environment Directory
Audioholics Buying Guide
Fast Company Talent & Careers Resource Center