I do not like automated submissions as they lead to spam, so let us talk about manual submission. There are primarily 2 types of manual submissions:

Manual Directory Submissions
In this type of submission, you go ahead and fill up forms set up by web directories. A web directory is to websites what a phone directory is to phone numbers. Web directories can be free or paid. I have found that there are many free web directories and a few exceptionally good paid ones. Also, though most web directories are generic, some are niche web directories -- for instance I have seen legal web directories, real estate web directories, health web directories and what have you. My experience is that manual directory submissions do not help in raising the search engine ranks of the websites significantly. But, they can certainly help search engines in understanding the theme of the website. This is primarily because your site will be listed in the directory on a page that is about tightly related sites.

Manual Article Submissions
Quite naturally, I am a fan of manual article submissions. I say that as I am creating this article for exclusive distribution by article submission sites. That you are reading this article is testament to the fact that word does go out and you can gain popularity by submitting articles to article submission sites. But, there are a couple of ifs and buts. First of all, the world of article sites is quite lopsided. For every good article directory there are a hundred junk sites. Make sure to do your research to ensure that you are not stuck with the junk kind. Second, if at all possible, try to submit unique articles to different article sites. At least make them a little different. The reason for this is that search engines such as Google have become very smart. They are able to read the same article on different sites and despite some of the surrounding text being different; they are able to tell that the article is a duplicate. What these search engines do is to relegate these duplicate pages to a supplemental or lower priority index. Hence the links on these pages will also get much less benefit.