Floating diode in a Sot23 package
If the common is connected to a low-impedance node you can leave it floating. If not, I'd short it out lest it act as an accidental antenna/detector. 

I'd also suggest using the single out of the pair that would be present if you bought the one-diode version of the 3-pin package (if possible), just for future compatibility. IOW if you're using the BAT54C or BAT54S, use pins 1 and 3 and either leave 2 open or short it to 3. If you're using the BAT54A you can't do this.