Google’s navigation menu is still not customizable. The app launcher interface allows Google to add many cool features like reordering apps, removing them or adding new ones, but for now they’re not available.
Carlos Jeurissen released a Chrome extension that lets you customize the app launcher. You can select from a very long list of Google services, including Google Scholar, Google Play Music, Google Keep, Chrome Web Store. You can also reorder the services or remove the Google products you don’t use often. The upgraded launcher has up to 5 columns and as many rows as you want, but I suggest to pick less than 20 services.
4/25 UPDATE: Google now allows you to rearrange the icons in your app menu in regular Gmail accounts. It’s still not available in Google Apps, but presumably it’s coming!