The only problem I had was with recursive requires, but I created a pull request fixing the problem, and the team was very responsive about getting it fixed. The fix was integrated and put out the same day, so I didn't have to deal with any delays.
My main concern is non-CommonJS libraries. I haven't really had any luck with any of the Browserify shim modules out there. Any jQuery plugin that I've used with Browserify I ended up modifying myself to support CommonJS. Even then, I'm not sure I was doing it right.
Any insight?