Linking to a web page other than a site's home page.

Deep linking has only begun to spark mild controversies in recent times as the Web has become more commercialized. In fact, one of the fundamental strengths of the Web is the ability for any public document to connect to any other public document.

The legality of deep linking has been called into question in several lawsuits involving well-known corporations. Opponents of deep links -- typically large corporations -- argue that deep linking unfairly eliminates the ability of the home page to contribute to brand building and ad serving functions.

Proponents of deep linking contend that the ability to link freely is central to the philosophy behind the public Internet. On a practical note, they also argue that a deep link is better than no link at all, and may even be more profitable than a home page link, especially if the target site has a poor navigational structure.

From www.marketingterms.com
/dictionary/deep_linking/

Google and the other search engines have improved their algorithms over the years and now use hundreds of criteria to rate the worthiness of a website. Unusual patterns raise sp,e doubt about the worthiness of a site. For example, a quality site, with naturally gained links would not normally have mostincoming links to their homepage. Naturally obtained links tend to point to a wide range of internal pages along with homepages.
Lets face it, you probably have enough home page links already. Deep links will help make your link building efforts appear more natural.
You cannot and should not have your homepage optimized for more than a couple of keywordphrases. Ideally, your SEO efforts should included internal pages optimized for different keywords. Internal directory links will help your search engine rankings.