Save saves your trace data so you can examine it later.
Save as template saves the trace document's instrument list as a template you can choose from when you choose Product > Profile in Xcode or File > New in Instruments.
If you find yourself constantly adding instruments to the trace or removing instruments from the trace, saving as a template frees you from having to add or remove instruments every time you trace. Suppose you're profiling the performance of an OpenGL game and you want to use both the Time Profiler and the OpenGL Driver instruments. You'll notice Apple does not provide a template that combines both of these instruments. You can set up your trace to use both instruments and save as a template so you don't have set up the trace every time you profile your game.