Plugins and loaders are easy to write and allow you to control each step of the build, from loading and compiling CoffeeScript, LESS and JADE files to smart post processing and asset manifest building.
Browserify does nothing client-side. It's only a server-side builder. If you want to load files from other domains, look at RequireJS. If you want to break your code up into multiple modules, look at RequireJS or Webpack.
RequireJS is awesome for bundling and managing dependencies in an async manner. But the server-side needs neither of this killer features. Because of this it's not as good if your building a library that should work on both client and server (i.e. PouchDB).