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Deselect All (Alt + E): Deselects everything in Hierarchy and Project views instead of having to click on an empty space. Useful in busy scenes.

Invert Active (Alt + A): Inverts the "active self" flag in hierarchy. Works on multiple objects in Hierarchy and Project views.

Remove Auto-Name (Alt + R): Removes the auto-naming addition on objects created by duplicating (Ctrl + D). For example duplicating object named "Fox" would create objects "Fox (1)", "Fox (2)" ... "Fox (156)". After duplicating, select the new objects and press the shortcut, all objects will now be named "Fox". This removes visual clutter and useless information. Works only on Hierarchy duplicates, not Project duplicates.

Duplicate Without Auto-Name (Alt + D): Duplicates selected objects in the hierarchy without adding the standard Unity postfix " (1)", " (2)" etc. This works only on objects in Hierarchy, having an object selected in Project view will instantiate it in the root of the scene, which may not be desirable. 

Multi-Object Rename Wizard (Alt + F): Opens a wizard that will take all selected objects and replace one string in their name with another. Objects that have the same name can be bulk-renamed in the Inspector without this tool, but objects that share only part of the name can not.
Copy / Paste Transform Values (Alt + C, Alt + V): Copies the local values of the Transform component of a selected object; Pastes the values into the selected object. Useful in situations where an object is duplicated, reparented and set to exact same transform values relative to parent as the original. Usual workflow would involve the lengthier Copy Component / Paste Component Values procedure.