I actually like the idea of extending the end of the counter and putting shelves underneath. I think visually it would extend the base cabinets. The shelves would be a nice way to store cookbooks or really pretty/exotic dishes. I just don't think 6" would be enough for books but may be okay for smaller special dishes. I'm sure someone else will have better input.

I like the idea of tucking a stool in there, too, especially if there is no other stool in the kitchen. It's always nice to be able to grab one and sit down. If your house is like ours, a stool gets a lot of action from our littles, and I'd love a dedicated place to tuck one away when it isn't in use. Depending on the style, a step stool that doubles with seating could go there and then be pulled out for reaching into the top shelves of pesky uppers (I'm kinda short.)

Is this in a good spot for a trash can? It would be so much less expensive to put a can under there in the opening than buying a trash pullout cupboard.

Here is a picture of book cubbies under a peninsula somewhat like you describe. It's in the comments section, the author is "Mid Mod Mom" http://www.houzz.com/ideabooks/414525/list/Show-Us-Your-Kitchen-

Here is a link that might be useful: Retro step stool chairs