In my off page optimization post, i mentioned the importance of gaining back links from other web sites to your website pages. It is also very important to have a proper internal navigation within the site itself. That is, your users can navigate the site, and all the time, they can find link to take them to any previous page in their path.
In this regard, i would recommend having a breadcrumb trail, that contains each page the user went through to reach his current page. Usually breadcrumb trail links separated by greater than sign “>”. Breadcrumb trail helps crawler to crawl your web site, and it distributes page rank among your web site pages.
Click depth is the number of clicks a user needs to click from a site home page to reach a page. Click depth has to do with ranking for almost all search engines. The more the user needs to click to reach a page, the harder he can find the page. Search engines consider this in some way in their scoring algorithms.
You should try to have your site navigation as easy as possible not only for search engine’s sake but also for user experience. You may consider having a site map with good hierarchy to help your users and search engine to find any page on your site easily. In case you have an enormous number of pages, you need to be careful when picking a pagination schema. The lower the number of clicks a user needs to click, the better for user experience and for SEO.
It is worth to mention that click depth is not related to where you save your files in your server. That is, if you store a file 10 folders deep in your server and you access it by one click, thats much better than storing it in the site root and the user needs to do 2 or more clicks to find it.