It's worth listing your comic in these directories - even if you don't make the top 100 people will still be able to discover your site. If you want to promote your comic further most of them offer paid advertising slots in the form of rotating banners. Most sites want a link button on your site in return.
Tthis is a huge directory of online comics which now has merged with Webcomics Nation to provide a number of webcomic information and hosting services- It has an bookmarking and update reminder feature which is useful if you are a webcomics reader. Their advertising consists of rotating avatars on the site and also puts your listing at the top of related search terms. It has a number of updating features including an automatic RSS update checker. They want a link on your site in return.
An online community, news feed, bookmarking feature and webcomics rating list - it has an automatic updating system for when you post new comics on your site (though admittedly I couldn't get it to work for mine). You can advertise on their site as well. You don't have to be the author of the webcomic to get it listed here.
one of the older webcomic lists that focuses on anthropomorphic comics but is happy to list non-furry comics as well - well worth listing your comic here.
A large automated webcomics hosting system. Joey Manley has recently opened free accounts - at the moment there is unlimited page limits and it makes automatic RSS feeds of your pages and will automatically update according to the calander dates you set for each page. if you have a paid account it also puts your comic add into rotation on the site every time you update. It also hosts the Talk About Comics forum and blog.
Ryan North's feed maker - it's easy to use and the basic account is free. You'll need to know some HTML as you need to paste tags into the code of your page. This allows you to set up feeds from your webpages, so people can view them on RSS aggregators or readers..An easy way to let people know you have updated.
A comic creators and fans networking system similar to MySpace but for comics. You can now host comic pages here, send out bulletins and leave comments for other creators - well worth joining if only to see what everyone else is up to.
Ryan North's targeted webcomic and small business advertising - you can advertise on other webcomic sites for a small cost a day - price is by auction and bidding can take a bit of time, but if you choose your sites wisely you will get more hits for very little money.
You can also advertise on your own site but unless you have a higher traffic site you may not get much return, but with the introduction of cent amount bids, most spots return at least a few cents a day..Banner and skyscraper sytle adds usually get you a better price than button adds.
One nice thing about Project Wonderful it is an easy way to support sites you like and get some advertising back in return - and I also found a lot of webcomics I really like simply by looking through their adveritsers.
Google Adds displayed on your website are free to set up, but webcomic authors report variable success with them. They don't pay out until you have acrued over a $100 so it can take a very long time to see any return - they also don't pay unless the adds are clicked on regardless of how many times they are displayed (leading to the incidence of "click fraud" where people click on the adds because they know they are going to pay out, rather than being interested in the site advertised)
But it's free to try so it couldn't hurt if you are trying to get a bit of money back from your webcomic..
As for as using them for advertising your webcomics, from the reports I have read it suggest that it isn't all that successful in driving traffic towards your comic..
There are lots of tracking programs which can give you details of visits and where the visits are coming from, very necessary to stroke the ego and show that your webcomicing strategies are working- I've used site meter so I can recommend it - its free and it's tracking details summaries are very easy to use. Other people seem to like Extreme Tracking though I haven't used it.
one of the older webcomic lists that focuses on anthropomorphic comics but is happy to list non-furry comics as well - well worth listing your comic here. 
