webpack: http://webpack.github.io/ jspm: http://jspm.io/
Nice introduction presentation: http://peerigon.github.io/presentations/2014-07-09-MNUG-webpack/
The watch seems intelligent in that it might be tracing the dependency graph. In my test case it seems to, at least. AMD and CommonJS modules are supported out of the box. In my test I was unable to get es6-loader working (see commit in link below).
Unlike jspm, it's not a registry. Instead it resolves dependencies from node_modules (i.e. npm) by default (like browserify), although according to this tutorial it's trivial to configure which directories the module resolver should read from.