Here are the new breaking changes in browserify v4. Most users should be unaffected.
require('stream') is now using readable-stream (but the classic-mode shim persists in stream-browserify just like in node core). This should result in much smaller files for all modules using a similar-enough version of readable-stream as browserify itself. Other modules should be relatively unaffected.
Removal of the previously-deprecated and obscure bundle.expose().
Previously if you invoked the browserify command without any entry files as arguments and stdin was a tty, stdin would be implicitly added as an entry file. This feature was causing problems so it has been removed. browserify#724 (comment)
In the run-up to the 4.0, module-deps got an extensive rewrite with minimal test changes. Mostly it was just getting really messy because it was a giant ball-of-mud closure instead of a more straightforward prototype-based implementation with more clearly-defined methods.
The module-deps rewrite was triggered by system paths showing up in build output but was fixed in 3.46.1. The solution actually didn't end up needing changes in module-deps as originally anticipated but module-deps was in dire need of a cleanup.