Much like the late Rodney Dangerfield, internal links get no respect.
Every time I hear an "expert SEO" rail on about the importance of inbound links above all else, I cringe. Not because it is an inherently wrong viewpoint, but because it takes the complexity of search engine optimization and boils it down to one factor. The success of Google has been hinged on its ability or failure to lower the strength of a single factor from being too influential, and although IBLs are still the single most important factor in most search algorithms, to make a link building plan for your website and not evaluate your internal linking structure is a mistake.
The first thing you must do is separate yourself from the ingrained concept that the web is a system of domains and sites. In search we must see the web as the search engines see it, as a series of interlinking pages. Granted factors such as domain age, and even where the site is hosted have weight, but in reality link equity rolls from page to page.
This means your website, has now become a much more powerful being, with x pages to disseminate link equity and relevance.
When I begin to work on a site I look at it in tiers. The first tier is your homepage. For almost every site on the web, their homepage is going to be the page on the site with the most equity. From there the pages in your homepage navigation (or any page linked from your homepage) becomes your second tier. The third tier is comprised of pages linked from the second tier, and so on. This is the way that link equity will be spread through your site, and it is the way that you should attack your internal link building efforts.
From here you should work with your keyword research to see what words are most important to your traffic strategy. If you have a great page written, with a great term that generates a ton of traffic, you will want to get an internal link to it on your homepage. This will promise this piece of content the most link weight possible from internal sources. This strategy becomes increasingly effective with low competition, long tail terms, that may need very little in terms of relevance in PageRank to climb to the top of the rankings.
You should work through your site from tier 1 to your last, linking to pages in descending value, using your keywords and matching content in the same manner. This will create a well structured use of your link equity from page to page. This is vital, because without it all of your link building efforts might be wasted as the link equity may not reach your powerful long-tails and deep pages.
Time and again I see sites with this issue. It is often the last thing that people think about in terms of making their site search engine friendly and highly marketable. However, a well structured internal linking strategy can make a large difference in your results from page to page, and an SEO strategy is usually won or lost in the small details.