I think that it is best to link to your index, as your index hopefully contains links to your inner pages...as search engines crawl your index links on other sites, it will lead the search engine spiders to your index page, and then the spiders will crawl the links found on your home page to your inner pages. This will also help spread your link juice around throughout your whole site.
Now if your index does not contain any links to your inner pages, I would suggest that you add some!
But the problem with targeting index page to get link for, is that one can not make use of any particular keyword for getting links. As index page contains many of the different pages content so it will not be easy to select any of one keyword from those content pages to get link with. So instead of this it will be more helpful to get link for the individual page with targeting particular keyword relevant to content.
Originally Posted by BiologyWebmaster