Please suggest, shall I submit my site in the directories which has not been indexed by Google? I’m really confused 
Are you talking about penalized sites or newly created?
Either way, sure why not, go ahead and submit it.
Tomorrow G. could crawl new site and remove penalty from the one it has punished.
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Is your website new as well or it is the old one? If your website is old enough and you have almost finished with submitting your website in all existing directories, you can go for it. But if your website is not submitted in old directories, submit it to only good directories. Check with the previous submissions in the directories you are talking about and then decide whether to submit your sites in these directories or not.
Directory submission, with the exception of DMOZ, is pretty much worthless as far as SEO goes anyway. If you absolutely feel the need to submit your site to directories and the stats showing what a waste of time it is can’t dissuade you, you should aim for the ones with the highest volume of traffic and where you can get the best position. It’s still no good for SEO, but you might pick up three or four actual visitors that way.
In terms of SEO, assuming you’re targeting an area where Google is the dominant search engine, there’s no point at all in getting placed on a directory that Google hasn’t indexed. How could there be? If Google hasn’t indexed it then it’s not going to look at the links on it.
With the exception of DMOZ???
What is so exceptional about DMOZ?
How one backlink it gives make it better than AMRAY Web Directory as for example,
where site owners are getting up to 10 backlinks including links to Twitter, Facebook etc.?
Ya, I know, another DMOZ discussion but… I hope Internet God will forgive me for that one.
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The reason that a link from DMOZ is worth a squillion and a half links from most directories and social sites is because they’re very hard to get. It’s one of the few directories that does seriously vet the links that it gives … so Google knows that for a site to be listed on DMOZ, it must be providing content of some value.
Most directory sites are not that picky. Some will accept any link they get. Others practise some level of authorial control but they are often lax and allow content that is scraped and leeched as well as link farms and heaven knows what other dodgy stuff. Out of date links are rarely checked and updated or removed. (Sure, there may be some minor directories that are better than this, but when they aren’t major players it’s hard for Google to get to know which ones are trustworthy).
Social sites are even worse. They are pitifully easy for authors to manipulate, which is why search engines really aren’t interested in them at all.
Granted DMOZ is best know but… and that is where we’re going in different directions.
It also bloated with dead and sometimes useless links, which as you know triggered G. to drop
that directory for good and talking about 1 single backlink (no more than that)… well, we have site
yahle,com with one backlink from AMRAY directory that has PR 2 and you know what is the best part
of that equation, yahle’s index page is blank. But then again, it says how G. PR system is useless.
Now if DMOZ can pull something like that, I would be first to admit that they are any good.
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