I've been working on getting my game to run in NaCl. I found that NGUI works almost perfectly in NaCl with one small change. In UIPanel NaCl needs to use the same code as Flash. Specifically, NaCl doesn't seem to support OrderedDictionary. The solution is to add a check for UNITY_NACL everywhere NGUI checks for UNITY_FLASH.

The only other issue I'm seeing now is that the speed of scrolling a UIDraggableCamera with the mouse wheel is off (way too fast in NaCl). I haven't looked into this yet. Either way, it's hardly a dealbreaker.