I very general approach would be to build links and target keywords with your inner, topmost hierarchical pages.
For Instance, if you had a pet-related site:
Your main site/home url would target keywords like 'Pets' 'Dogs' 'Cats' etc..
The your would rank inner categorical pages like 'Dog Grooming' 'Pet Nutrition' 'Cat Posts' 'Dog Training' etc...
I believe that these types of site links are largely related to how people use your site though, which is interpreted by gxxgle. The best way to influence this would be to build value and incentive for people to visit your subpages directly.