I have been a webmaster for the past 2 years, now recently google has introduced a new algo in their armoury, i.e supplemental results. A content is duplicated or insufficient links. Its one way contradictory to its previous algo. Because google said having thematical links will increase the chance of rankings. I have done that according to google words but i have a website it has more than 500 pages, due to this supplemental result concept 400 pages are gone into the shell i mean de promoted from the results. I assure all the contents are unique and written by our team. Only thing im still confused whether if someone copies the content of my website, then who should be penalized for the act, google software does nt seem to realize that , it has punished me hate this new supplemental results concept.

Google supplemental results have been around for a very long time (at least from what I can remember). Their purpose is to have a place in Google's index for webpages that don't have enough inbound links, etc to be worthy enough to be in Google's regular index.

Make sure you have a lot of inbound links to all different pages throughout your site (not just your homepage), and make sure you have a solid linking structure and navigation among all your pages.

Yes thanks for your reply, i can understand about linking structure and navigation i will check at it. But google says only linking to related theme pages or related content will give the page more chance getting into top results. But for ex i have topics on technology, software i relate all the software topics into one, technology articles into one but in software section there will no linking structure to technology articles,My question again is Did u mean i should link all the pages in my website even the contents are unrelated? Like a page from technology should link to software page.

I don't think you have to worry about technology and software would give you anything to worry about - they are similar enough topics. I would start to worry when you're advertising for a shoe store :)