Will your site be penalized for automatic directory submissions? On the surface, it's almost an absurd question. The search engines only see a backlink from a directory, they have no way to determine that the link was obtained with an automatic submitter. Even if they could identify automatic submissions, why would they care?
While it seems like an obvious answer, there is a lot of misinformation floating around the SEO community regarding automatic submissions. "You should always submit manually" is repeated in some forums like a mantra, without any actual evidence that it is true.
Again, why would the search engines even care how you submitted your site? It's up to the directory owner to either approve or reject your submission. If the directory chooses to list your site, it's unlikely that a search engine would somehow penalize you for that link.
So it's the directory owners themselves who may take issue with your automatic submissions, if they're done the wrong way. Automatic submission can be very quick and effective, but it does require some common sense. Obviously, one thing you don't want to do is keep submitting to the same directory over and over again. Your IP will probably be banned after a while and the directory owner may add image verification or other measures to defeat future automatic submissions.
A good automatic submission program should not leave any identifying footprints. Be careful when using free tools as sometimes they add a "submitted by" tag somewhere in the description. This problem is more common with article submitters because it's easy to stick a tagline in the author's bio box, but it still deserves a mention here.
Improper category selection is another quick tip-off that your submission came from an automatic submission program. The problem is that most of these programs try to read the category on the fly, many subjects can be listed in different categories or subcategories. For example, an automotive site could fit into Blogs/Automotive, Recreation/Automotive, or Shopping/Automotive. In this case, the software may find the "Blogs/Automotive" label first and submit every car-related site into that category, whether it is a blog or not.
Another thing not to do is submitting tons of subdomains or inner pages from the same site. This is a common tactic for spammers and most directories prohibit it. If you must submit subdomains or subpages, there are many directories that will allow this for a small fee. Submitting them without permission will only irritate the directory owner and probably get you banned.
Automatic submission software can actually improve the quality of your directory submissions, along with saving lots of time. A good program can help avoid common reasons for automatic rejections like typos and incorrect description length. Once you enter your site information in the submission software, it will submit correctly to all of the directories, eliminating all those extra chances to make a mistake.
Overall, automatic directory submission by itself cannot hurt your ranking in the search engines. You will almost always gain ranking and Pagerank anytime you submit to web directories, unless you are submitting to low-quality sites. Don't abuse the automatic submission tools and you won't have any problems with search engines or ticked off directory owners.
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