Google Penalization on the Homepage (Google Penguin related?)

It really depends on your individual site now. Seo is becoming a very diverse subject and there are lots of things that can affect websites.

It could be panda has filtered the site (they refreshed a few days ago), but no one here will know for sure unless they look through the site in detail, so that's what you need to do.

Check your anchor text distribution with tools like opensiteexplorer.com and check your onpage for duplicate content issues, lack of substantial original content and too many ads above the fold and any other onsite quality issues what could be easily filtered out by Google like too many links or stuffed content in the footer.

You site could fit a profile Google aren't liking so make it as unique as possible, including the backlinking.

Yes I believe they can, without some sort of deep link ratio if you have say 400/1000 links with zero links to your internal pages it could be a problem.

I've seen sites affected by penguin that had 100% links to their homepage, no brand.com links but all of their links where nearly unique. 8000 in total with different but similar anchors. They dropped around 5 pages, not alot in comparison to sites with 90% exact anchors but still an issue.

In terms of your link building campaigns you could be reaching bordline - not using enough branded terms or some of your keywords may be a little aggressive or perhaps you are not rotating enough keywords, like building 5 links with one and 10 with the other, you need to rotate them heavily. Also you could have too many links and not enough anchor text variety, if you have 200 links then 75% of them need to be unique.

From what you've said it seems like the issue and you know the answer.. Just build a few deeplinks, add more secondary, branded and generic keywords to your homepage.

No, Google does not just punish sites for a large percentage of links coming to their homepage. If they did, 95% of small businesses wouldn't rank for anything. A local lawyer, dentist office, plumber, etc... Nobody is linking to their internal pages.

Now there could be other criteria. Maybe if a site has 1000 pages and 90% of the links are to the homepage, they see that as an issue. I don't know. I have not researched that.

You could build them up in a silo structure of related pages:

Post6=>
----------Post3=>
Post7=>---------- Post1=>
----------Post4=>---------Homepage
Post8=> ----------Post2=>
----------Post5=>
Post9=>

and then link post 1/2 to your homepage with your keyword and build loads of high pagerank backlinks to your internal pages. It doesn't really matter what the anchor txt is then... you just want the pagerank traveling up to posts 1&2. Do this for every group of similar posts you have on your site, putting the more competitive ones closer to the homepage. If your rankings can come from your internal pages and deep links then yes it will look alot more natural...

Yeah they definately have their uses but they won't provide a ton of pagerank.

If you site has useful content like tutorials then the internal pages are more likely to be bookmarked than the homepage and the opposite is true when you find a small site or an ecommerce store. Sometimes people will even bookmark your internal pages with your brand.com link as the title...

If you look at your anchors and your brand.com anchor isn't your most popular (which I suspect it isn't) then use bookmarks with yoursite.com to your homepage and then a mixture of keywords to your internal pages.

You need to remember that your most popular links won't only be your highest amount of links but they need to be from a wide range of ip address' and c-blocks, so this is another good use for social bookmarking (link diversity) as well as social signals.

I would do a nice mixture, bookmarks and hunt down a handful of good high pagerank links for your internal pages, only 3/8 links per page.

You need to be creative about the way you hunt down these websites. For example it's no good searching for blogs on google.com you need to go to google.it/ncr then search.

You can start with your main keyword, take for example " technology".

inurl:"tecnologia"

and the you need to add some footprints to refine your search criteria:

inurl:"tecnologia" "Commenti"
inurl:"tecnologia" "Commento"
inurl:"tecnologia" "Commenta l'articolo"
inurl:"tecnologia" "Login Per Inviare Un Commento"
inurl:"tecnologia" "Login O Registrati Per Inviare Un Commento"

The broader the search in terms of the topic (technology) the more sites you will find etc.. Once you find a site that is both dofollow and auto approve then note down the charcteristics. Is there a common denominator that you can use to find a whole group of websites?? i.e; "powered by xxx" are there generic words that appear onpage and might appear on the pages of other websites?

So you can refine your footprints over time. Maybe sometimes you will find another commenter that leaves comments on alot of Italian blogs, so you can use their keywords as your footprint, for example:

"Entra Per Commentare" "the keyword"

Instead of looking through people backlinks this is what I mainly do. I find a blog with a comment that matches my criteria (mainly pagerank) and I refine the footprints and a few variations to surface all the sites I'm looking for.

Once you have found the right footprints, you can scale it up by entering it into scrapebox, removing the duplicates and filtering out the high pagerank blogs.