Has directory submission hurt my site?

There's a lot of things that affect your SERPs, and hence the amount of organic traffic that you get from search engines. The key here is that you bought the domains rather than registered them. Therefore you don't know what promotion the previous owner(s) did. Could be that they used the domain for blackhat tactics (Blackhat SEO seem to favor cheap .info domains)
Could also be that your domain was submitted to 200 FFA linkfarms!

 

Do manual submission one by one to free directories,because sometimes automatic submission wont list/submit your site in their directories.

 

Yes it does and yes they can it's called "bowling". I 100% agree ffa is bad very bad.

 

I think this is a misconception, I don't think the "average" user has the ability to add links too fast ESPECIALLY if you are adding links manually unless you have a team of 20 people doing it.

200 links for a new site is nothing especially when they are directory links.

I have had new sites hit the front page of Digg and receive 100s of backlinks in just a day or two (due to bloggers and forums).

I even used auto-mated tools and have never hit this "magical" threshold of too many backlinks too quick.

 

some of the paid submission is quite cheap and i am keen, but i am also afraid that it will hurt my site ranking

 

There is a theory calling "Google Bowling" which says that someone can harm your site by putting your backlinks on bad sites. But there is also a theory of Sandbox...which was said (M.C. on his blog)) that it doesn't exist.

It is not logical that someone can harm your site with backlinks. But if anyone can prove this, I can accept it.

 

well in the beginning it takes time and sometime even there are almost no any visitors. Good Marketing,Content,Metaphors are to be consider in beginning and there you go

 

Your site is quite simple and seems like an ordinary software site which is just decompiled with difference and site doesnt seem to be holder of professional viewing software
Cheers