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Hi Sida,

Are you talking about backlinks? If so just use opensite explorer, Majestic SEO or Ahrefs. Or just good old Google Webmaster Tools (links to your site). If you are talking about website links, you can use internal link analysis software like Xenu link sleuth.

Are you continuously adding new pages to the website each month?  If so, you could be diluting your domain authority. So when google caches your website, the pages have less authority than the last time resulting in a drop in rankings.

You say since a while, how long are we talking? If it is over the last two months you could be looking at a penguin 2.0 issue. If you have no issues with your back links I would do a check for over optimisation on your landing pages. The easies way I find to do this, is by, hitting cntrl +F and typing in the the keyword. Next click the highlight button. This will clearly show you how many instances you have of a certain keyword on each landing page. If half the page is highlighted then you know you need to write some new content.

Yes I agree with Ellison here. There is no perfect % keyword density in my opinion. I generally like to get 2-3 keyword mentions per 300 words.

If Google is still indexing past page 1 of cat pages, have you gone into WMT's and removed URLs from the index?