If you’re interested I’ll let you know if we come across something that is interesting.

I can tell you one thing though.. nofollow tags are not that nofollow. It really depends who gave the link the nofollow tag. These links may not give you PR or anchor text (but frankly I do not know this because I have not had the time to test all this), but it does not necessarily influence your ranking poorly. Or rather I can say from experience that certain nofollowed links definitely have had a positive impact on google. (and since we have only a few external links yet, I can be 80-90 % sure when a link has impact and which one it was). Oh… and I am not talking long tail either, and neither am I talking about being able to get into the top 10.. but for a pretty competitive 2 keyword sets, it can help your home page get from not listed at all (not even supplemental) to top 200.

Let’s look at Google and Ask. Google divides the Web into two indexes. They fully parse the Main Web Index but only partially parse the Supplemental Web Index. Links in Supplemental Pages don’t pass value — if your Supplemental Pages link out to other sites, those other sites won’t receive any anchor text (and probably don’t receive any PageRank).

But Google will still follow your internal links and add your internal pages to the Supplemental Index. They’ll also follow your outbound links and add those pages to the Supplemental Index. So your internal links work no differently from your outbound links.

On the other hand, if you have a page in the Main Web Index, you may be able to link from it to your other pages and get at least some of them into the Main Web Index. Matt Cutts put it this way: “You get so much (Internal) PageRank to spread across your pages. The more PageRank you have, the more pages you get into the Main Web Index.”

Of course, you have to have good internal linkage. In practice most business sites are small enough that only a few inbound links (that pass Internal PageRank) are needed to get them into the Main Web Index.

Ask, on the other hand, will parse your site into topics. It uses a mix of on-page factors and internal navigational links to figure out how many of your pages are more relevant to Topic A and how many are more relevant to Topic B. It’s kind of cool to see that they can analyze a site structure so well. But that depends a lot on your internal linkage.

On the other hand, your internal links may not be sufficient to help your pages rank well on Ask for those specific topics. You may still need topic-relevant links from other pages that Ask has qualified for those topics.

So those are two examples of how search engines may distinguish between internal links and external links. But you should be careful not to read too much into those examples. They only illustrate possibilities, not definitive rules. The search engines have very sophisticated algorithms.

Can I make any assumptions about this: e.g. within the text more relevant than in footer but perhaps less relevant than in top menu ?

Are there some general rules of thumb for this.. or is it really about.. trying it, see what happens and try again ?