When I was just starting Eikasia, I didn't get a steady stream of clicks from any one thing. I got them from a bunch of sources, some of which I had to pay for.
Project Wonderful can be good if you advertise on related webcomics with moderate to high-traffic. I also participated in banner exchange programs like nuts. I submitted to every relevant link directory I could find. I also updated every profile I ever had online to include a link to my story. I also put the link in my email and forum signatures. For the latter, I heard that naming your link something like "My online story" (like I did below) makes it easier for it to turn up in searches involving those terms.
Networking with those who make their writing available in a similar way is an obviously good thing, too. These past few months have made it harder for me, but when I first started writing Eikasia, I was getting involved with weblit/webfic community affairs whenever I could. You form relationships with others who sympathize with your struggles, and help you when they can--provided that you're kind enough to return the favor. Direct link trades from people outside the community are nice too, if you can find willing affiliates with decent traffic. (I have two or three affiliates and I get clicks from them every month)
Underestimated ways of getting readers, and thereby getting comments, is pimping your work to your friends and family. I earned a number of my readers through their word-of-mouth.
Get involved with another online writing community. One place in particular is Writersbeat.com--I used to post there all the time and it has alot of great people who not only will show interest in your work, but help you too.
Now that I have two complete stories finished in my series, I was able to add to free-online-novels.com and online-novels.blogspot.com which give me tons of visitors every week now.
And...those are all the things I can rattle off the top of my head. Does that help?