I can't imagine dropping a series of <script> tags on a page to build a minimally complex website anymore. I've got used to browserify and so I can't go back to building my fancy 3D thingies like it was 2012 all over again.
So I made this minimal template that sets the bare minimum you might need to build a three.js powered site using browserify via gulp. That lets you use any other npm-based modules and libraries you want! So your code should not be messy and/or a tremendously big file with everything tucked on it.
There's also some extra help like a file watcher... and not much more, really.
Do let me know if you use it for something cool... or if you can/want to help on this issue! :-D