BookShelf now requires you to also download SQLibrary from here and put it in your plugins folder.

Sorry it has to be that way. PatPeter, (the now-owner of SQLibrary, the library BookShelf relies on for its databases) has informed the BukkitDev staff that he does not want developers including his class files into their plugins, and instead they all must depend on his plugin. This means you are now required to download his plugin and install it if you want BookShelf to work. I am working on a custom library to avoid this, but until then, if you want to complain and tell PatPeter how inconvenient this is, feel free to write on his plugin wall here.

If you get an error when starting bukkit along the lines of "NoClassDefFoundError," this is because you have not downloaded and installed PatPeter's SQLibrary plugin.