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Here's why I think run is not necessarily a bad idea. Since the question didn't specify why run is a bad idea, I'm forced to speculate that it's because it's ambiguous. Here are some arguments for the tag:

1. Many new linux users struggle with the execution of binaries. This ranges from the need to chmod the files to prefixing ./. A user who doesn't know how to execute a binary isn't going to know that they should tag the question with, for example, chmod.
2. Executing a binary in windows is often not trivial. There can be a range of issues from compatability and missing libraries to permissions issues. Users might not always know what is causing the problem so expecting them to correctly tag the question with the specifics of the solution is unrealistic (If a user knew that the problem related to a compatability issue they'd have solved 80% of the problem in many cases).

As to why it is a bad idea; well it is ambiguous and run could mean just about anything. In this regard I don't think Gaurav's suggestion of a binary-execution tag is a bad one; it removes the ambiguity and lets users still tag the question when the specifics of the root cause are unknown to them.