as I landed here with the same warning message, I could fix my problem as following:
in my case the root cause, why the clip-analysis-tool was not working properly without the message „000117: Warning empty output generated”, seemed to be an entry for "definition query" in the layer properties: I just want to use a subset of my input features. After exporting the desired subset into an extra feature class and using this one as input features the problem was fixed.
My working environment:
• ArcGIS 10.2 Advanced
• Input features: File Geodatabase Feature Class, WGS84
• Clip features: Shape File Feature Class,WGS84
• worked with Python Window
• Environmental settings: no extra settings
Thanks everyone for helpful hints! I was trying to run clip in ArcMap 10.3.1, using a query layer county polygon to clip a statewide road feature class, and kept coming up "empty". Converting the query layer to a standalone single polygon feature class did not solve the problem, but running the Repair Geometry tool on both single county and road feature classes did. I was successful running clip tool from ArcCatalog.