Earlier in this thread, Jeff gave us a link to a directory submission service. If you click on that link, you will get some great submission insight.
When you submit your website to an online directory, what you are doing is requesting a listing, or brief profile of your site, to be included in that directory. Most directories have specific guidelines of what they will and will not accept. Therefor, most directory owners will not include your site in their directory until they have actually clicked your link and reviewed your site to make sure it fits their guidelines. Depending on how many submissions they receive, it could take a few hours to several months before they review your site, make a decision and advise you.
So, whether you do manual submissions, or you use submission software like I do, or you hire someone to do it for you as Jeff has suggested, you make your submissions and you take your chances - there are no guarantees of acceptance in any particular directory. However, you can improve your chances by obeying the guidelines.
If you don't follow the guidelines, or if you submit to inappropriate directories or inappropriate categories within a directory, or if your site doesn't meet certain quality standards, you stand a greater chance of being rejected.
That's where I say that, if you have a high degree of rejections, then maybe there is something you can or should be doing differently to improve your chances of acceptance in the directories.
I just found my Directory Submitter affiliate link, if you are interested in checking out the sales page. I've used the service for about 10 months, but haven't actually promoted it for affiliate commissions! I guess now that I know I am happy with the service, I should tell others.