I love bookshelves, they bring order and sometimes drama to a room. And they aren't just for books! Sometimes clients get overwhelmed with how to arrange the small accessory items or how books should be arranged (by height? by color?).
The first thing I recommend is to completely empty out the shelf and start fresh. Determine what things stay and what goes, and if there are other items from your space that you'd like to display then bring those out at this time as well.
The final look should showcase your books and accessories and be restful on the eye. There are many ways to arrange books; by color, size, type, etc. I unusually arrange by the type of book first, (gardening books in one area, for example) and within that I'll arrange by size. For pops of color I will stack a grouping of red books horizontally and place an interesting accessory on top.
I like to alternate books with accessories or pictures and play around with it until the "balance" looks right. In the end, your shelves should have an organized, balance feel, and feel cohesive to the eye.