Really appreciate the informative reply. Like you I'm currently the SEO for an ecommerce store which has so many variations and sections that it can be a real headache. We've made good progress flattening the sections and I think from what you said, and a Matt Cutts article I just read on the subject, I'll remove the nofollows, leave Google to it, and take things from there.

Thank you for the link, I had a read and I've also been making the nofollow adjustments I suggested above.

We have tried to break down the menus into simple, managable chunks. Therefore we are really only linking to important categories. That said we can obviously deem some to be more important to us than others. As such i've employed nofollow tags within the menu on the links which won't generate as much ROI.

Is there any problem with having a nofollow to a certain page within our menu, and then a followed link to that same page within the main page content?

Hi,

We have a site with 7 top level sections all of which contain a large number of subsections which may then contain further sub sections.

To try and ensure the best user experience we have a top navigation with the 7 top level sections and when hovered a selection of the key sub sections.

Although I like this format for the user as it makes it easier for them to find the most important sections / sub sections it does lead to a lot of links within every page on the site. In general each top section has a drop down with approx 10 - 15 subsections.

This has therefore lead to SeoMoz's tools issuing its too many internal links warning. Then alongside this I am left wondering if I shouldn’t have to many links to my subsections and whether I would be better off being more selective of when I link to them. For instance I could choose the top 5 sub sections and place a link to them from our homepage and by doing so I would be passing a greater amount of link juice down the line.

So I guess my dilemma is between ensuring the user has as easy a time traversing the site as possible whilst I try to keep a close watch on where, and how, our link juice is distributed.

One solution I am considering is whether no-follow links could be utilised within the drop down menus? This way I could then have the desired user navigation and I would be in greater control of what pages link to which sub sections. Would that even work?

Any advice would be greatly appreciated,

Regards,

Guy