Radiant floor heat, nicer windows, moving pipes to avoid soffits, putting laundry somewhere convenient, upgraded faucets/shower fixtures, deliberate well designed landscaping, layers of lighting thoughtfully designed and fixtures from higher end companies (you can always tell the plasticy fixtures even from 20 feet away), a couple nicely constructed built-ins, nice door hardware, heavy, nicely made, interior doors (tru-stile), making sure the details make sense and things look finished (for example, not terminating backsplash tile with a raw tile edge on the top, but instead having a shelf, decent looking bullnose, cabinets, etc.