Off the top of my head,
1) Anything low level hardware (reading data via USB, or pushing data into HDMI, for instance)
2) Interacting with ANY hardware that's not explicitly supported by Javascript. Try creating an HTML5/JS scanner app.
3) Writing super-fast CPU-specific code, think Assembly language. That's the reason there are no HTML5 apps of the Photoshop caliber.
4) Disk access. Try creating a Javascript-based antivirus. Or an app that watches for changes in a certain directory.
5) Internal network access. Try writing a JS app interacting with your localhost or TCP/IP or UDP.