Waterproofing shower
If you mean what mortar to use before applying waterproofer (e.g. Redgard), then use unmodified with an alkali-resistant cement board tape.

If you mean what kind of mortar to use after the application of waterproofer (i.e. to apply the tiles), then use whatever mortar is correct for the tile of your choice. 

For instance, larger or natural tiles usually need a modified mortar, while smaller tiles can use unmodified just fine. The packages of mortar will describe their appropriate tile use.