Maximizing the effectiveness of internal links

Yes there is...
The internal linking structure can:

1. Insure that your website gets properly spidered and that all pages are found by the search engines
2. Build the relevancy of a page to a keyword phrase
3. Increase the PageRank of an internal page

Here is how the internal linking structure can affect these areas and how to maximize the effectiveness of the internal linking on your own website.
Getting Your Website Spidered
Insuring that every page of your website gets found by the search engine spiders is probably the simplest thing you can do for your rankings. Not only will this increase the number of pages that a search engine credits your site with, but it also increases the number of phrases that your website has the potential to rank for.
I have seen websites that, once the search engines find all of their pages, find that they are ranking on the first page and seeing traffic from phrases they never thought to even research or target.
This may not necessarily be the case for you however having a larger site with more pages related to your content will boost the value of your site overall. You are offering this content to your visitors, so why hide it from the search engines.
Pages can be hidden from search engines if the linking is done in a way that they cannot read. This is the case in many navigation scripts. If your site uses a script-based navigation system then you will want to consider the implementation of one of the internal linking structures noted further in the article.
Additionally, image-based navigation is spiderable however the search engines can't see what an image is and thus, cannot assign any relevancy from an image to the page it links to other than assigning it a place in your website hierarchy.
Building The Relevancy Of A Page To A Keyword Phrase
Anyone who wants to get their website into the top positions on the search engines for multiple phrases must start out with a clearly defined objective, including which pages should rank for which phrases. Generally speaking it will be your homepage that you will use to target your most competitive phrase and move on to targeting less competitive phrases on your internal pages.
To help build the relevancy of a page to a keyword phrase you will want to use the keyword phrase in the anchor text of the links to that page. Let's assume that you have a website hosting company. Rather than linking to your homepage with the anchor text "home" link to it with the text "web hosting main". This will attach the words "web" and "hosting" and "main" to your homepage. You can obviously leave the word "main" out if desirable however in many cases it does work for the visitor (you know, those people you're actually building the site for).
This doesn't stop at the homepage. If you are linking to internal pages either through your navigation, footers, or inline text links - try to use the phrases that you would want to target on those pages as the linking text. For example, if that hosting company offered and wanted to target "dedicated hosting", rather than leaving the link at solely the beautiful graphic in the middle of the homepage they would want to include a text link with the anchor text "dedicated hosting" and link to this internal page. This will tie the keywords "dedicated hosting" to the page.
In a field as competitive as hosting this alone won't launch the site to the top ten however it'll give it a boost and in SEO, especially for competitive phrases, every advantage you can give your site counts.
Increasing The PageRank Of Internal Pages
While we will be discussing PageRank (a Google-based term) here the same rules generally apply for the other engines. The closer a page is in clicks from your homepage, the higher the value (or PageRank) the page is assigned. Basically, if I have a page linked to from my homepage it will be given more weight that a page that is four or five levels deep in my site.
This does not mean that you should link to all of your pages from your homepage. Not only does this diffuse the weight of each individual link but it will look incredibly unattractive if your site is significantly large.
Figure out what your main phrases are and which pages will be used to rank for them and be sure to include text links to these internal pages on your homepage. It's important to pick solid pages to target keyword phrases on as you don't want human visitors going to your "terms and conditions" page before they've even seen the products.
If that hosting company noted above has a PageRank 6 homepage, the pages linked from its homepage will generally be a PageRank 5 (sometimes 4, sometimes 6 depending on the weight of the 6 for the homepage). Regardless, it will be significantly higher that if that page was linked to from a PageRank 3 internal page.
How To Improve Your Internal Linking Structure
There are many methods you can use to improve your internal linking structure. The three main ones are:

1. Text link navigation
2. Footers
3. Inline text links

Text Link Navigation
Most websites include some form of navigation on the left hand side. This makes it one of the first things read by a search engine spider (read "Table Structures For Top Search Engine Positioning" by Mary Davies for methods on getting your content read before your left hand navigation). If it is one of the first things the search engine spiders sees when it goes through your site it will have a strong weight added to it so it must be optimized with care.
If you are using text link navigation be sure to include the targeted keywords in the links. Thankfully this cannot be taken as meaning "cram your keywords into each and every link" because this is your navigation and that would look ridiculous. I've seen sites that try to get the main phrase in virtually every link. Not only does this look horrible but it may get your site penalized for spam (especially if the links are one after another).
You don't have to get your keywords in every link but if workable, every second or third link works well. Also consider what you are targeting on internal pages. If your homepage target is "web hosting" and you've linked to your homepage in the navigation with "web hosting main" which is followed by your contact page so you've used "contact us", it would be a good idea to use the anchor text "dedicated hosting" for the third link. It reinforces the "hosting" relevancy and also attaches relevancy to the dedicated hosting page of the site to the phrase "dedicated hosting" in the anchor text.
Footers
Footers are the often overused and abused area of websites. While they are useful for getting spiders through your site and the other points noted above, they should not be used as spam tools. I've seen in my travels, footers that are longer than the content areas of pages from websites linking to every single page in their site from them. Not only does this look bad but it reduces that value of each individual link (which then become 1 out of 200 links rather than 1 out of 10 or 20).
Keep your footers clean, use the anchor text well, and link to the key internal pages of your website and you will have a well optimized footer. You will also want to include in your footer a link to a sitemap. On this sitemap, link to every page in your site. Here is where you can simply insure that every page gets found. Well worded anchor text is a good rule on your sitemap as well. You may also want to consider a limited description of the page on your sitemap. This will give you added verbiage to solidify the relevancy of the sitemap page to the page you are linking to.
Internal Text Links
Internal text links are links placed within the content of your work. They were covered in last week's article on content optimization, which gives me a great opportunity to use one as an example.
While debatable, inline text links do appear to be given extra weight as their very nature implies that the link is entirely relevant to the content of the site.
You can read more on this in last week's article.
Final Notes
As noted above, simply changing your internal navigation will not launch your site to the top of the rankings however it's important to use each and every advantage available to create a solid top ten ranking for your site that will hold it's position.
They will get your pages doing better, they will help get your entire site spidered, they will help increase the value of internal pages and they will build the relevancy of internal pages to specific keyword phrases.
Even if that's all they do, aren't they worth taking the time to do right?