The primary problem I see with the browerify approach that was outlined is that it makes it much harder to debug your code in the webconsole.

By concatenating everything into a single file and loading that into the browser, you have to do the math in your head to figure out which file the code in question is in. Also, if you have a huge project, the watchify process really starts to slow down development as you are constantly waiting for it to do the concatenation.

I go with the requirejs/r.js approach. During development, requirejs effectively adds script tags to the specific files into your dom and loads your source code directly. No need for a watchify process. When you have a javascript error, the webconsole shows you exactly what file the issue is in. For deployment into production, r.js does the concat and I just load a single file. This unfortunately makes it harder to debug production, but that's the tradeoff. =(

Neither approach is perfect, but it is the best we have right now. I'd love to see someone come up with something that solves all these problems, is well documented and easy to work with.