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It largely depends on the effort. For LEED or Code compliance we've typically stuck to TMY3's as an 'official' source for weather data. For climate analysis or other predictive studies, we have used TMYx files; either in isolation or as a comparison to TMY3.
While not sure LEED or Code would object to the TMYx files (since they're the same in both Proposed and Baseline models), we havent pushed it.