Manual search engine submission is the best, effective and preferred method when it comes to submitting your website in the search engines. Search engines expect every details of the site to be filled in manually through their website mechanism. Automated submission through back door is considered as a SPAM in most of the popular search engines and directories.

There are hundreds of general and niche search engines which are eager to accept your website if you submit the required information in the right category according to the submission guidelines. The question is how you are going to do the search engine submissions and which search engines are you going to submit in? Certainly you dont want to submit your mortgage site in a "health directory or place it in the sports category of a general web directory.

You may have come across

Completely automated search engine submission service that submits your site to 90,000 search engines on a click of mouse ... IN SECONDS!"

and lot of other softwares which claim to automatically submit your website to thousands of search engines and directories. The rates of these submissions are very cheap and so is the result of these submissions. Chances are your website will be blacklisted by some of the popular search engines and directories. Consider the facts before you utilize a software or service to do automatic search engine submission.

Every search engine and directory is unique and the have various features which differ in

Different categories and sections. (Some may have as less as 12 main categories while others have more than 3000 categories classified into sub categories and inner categories. The category names are not consistent across the directories)
Different types of form input. Some search engines will ask for a very few details of your website whereas a dedicated account is needed in others for submitting your website. You need to do a detailed registration by providing phone numbers, address etc.
Registration and confirmation methods. Most of the search engines and directories need a confirmation from your email to avoid automatic submission.
CAPTCHA (IMAGE Confirmation) A picture with numbers which have to be manually entered. This is also to avoid automated submission.
Approval of your website.
Maximum number of submissions per user (some of them restrict to a single submission per user)
Frequency of submission..
The popular search engines and directories are opposed to automated submissions and it is considered as a SPAM. No automated software or service can take into account the above different features of search engines and directories while submitting the web sites. The fact is most of the directories do a manual review on the submissions and will find out the automated submissions sooner or later and block them.

What is manual search engine submission and how is it better than automated search engine submission?

Manual search engine submission is the process of analyzing where and what to submit in the search engines and directories by experts and doing each and every submission by hand ensuring a good acceptance rate for your website.

Manual search engine submission involves

Analyzing your website, doing the submission text with title, description, key words and creating a unique account.
Collecting the appropriate search engine and directories for submission and submit the website in the right category.
Modify the submission text as per the need of various search engines and directories.
Confirming the submissions (Image confirmation, email confirmations) wherever needed and co coordinating with the editors of search engines and directories whenever required.
The advantage over automated search engine submission is

First and foremost, manual search engine submission is the only acceptable method of submission to a search engine or directory. Automated article submission is considered as SPAM which is obvious from the various confirmations implemented by them.
A directory is organized into categories and subcategories. Editors review each submission manually and evaluate the submission. In manual search engine submission the websites are submitted in the related directory, search engine under the right category which is not possible in the case of automated submission. Automated software can't adequately submit to any article directory because it cannot study the directorys structure and decide which category is best suited.
Websites are submitted according to the different input systems of various directories by manual submission. Whereas automated submission just posts a set of predefined data irrespective of the input fields which results in an incomplete submission followed by rejection.
No search engine or directory is skipped in manual submission. Any Image confirmation (CAPCHA code) and email confirmation is done immediately which is not possible with automated software. Incase for any reason the search engine, directory is down or the website submission is not through, then it will be done another time.
More emphasis on niche search engines, directory related to your website theme.
Very high acceptance compared to an automated search engine submission.
Manual search engine submission with screenshots
Why submit to search engines