Home page links are good but links to other pages in your site are also very important. They help search engines know what the pages are about, they raise these pages in the rankings, and increase indexing of deep pages. They are also much more genuine looking, since when other people naturally link to your site they will usually link to a particular article or feature in the site rather than to the homepage itself.
Links to deep pages of your site are very important. The business is that Google separates every page on the world wide web as individual page. For example there is no any connection for google robots between yoursite.com and yoursite.com/page1. These pages are independent for its perception. Everything depends on linking from your home page to deep pages of your site and backlinks.
I feel its very important to get links to your inner pages, if you have thousands of backlinks all to your homepage it looks unatural, of course some places providing you with a backlink will only allow homepage. But where possible, spread it thoughout the site.
We recommend our link buyers to place about 30% of all links to their homepage and 70% to their deep pages - it looks more natural.