SAP2000:

This program is primarily used for gravity analysis and design

This tool is often utilized for smaller structures, or portions of a larger structure. 

It is great at handling complex geometry as it offers users a lot of different element types and a lot of customization with regards to meshing options.

It can also be used for wind analysis and for more simplified seismic design procedures. However, it will take more data post-processing to retrieve the desired results for story drift, story shear, base shear etc.

It lacks some of the simplicity that ETABS has of discretizing the structure into macroscopic elements.

ETABS:

This program is most utilized for handling large scale seismic (or wind) projects, including those that involve Non-Linear modeling.

It allows for more simplified modeling of the entire structure, enabling the designer to focus on macroscopic performance targets

It is well equipped to handle simplified lateral procedures, Push-over analysis, Response Spectrum Analysis, and Response History Analysis.

The data output options are much more conducive to lateral design

Please note that there are likely are some finer points regarding the differences between each program in regards to the analysis engine and solver. This is something only some folks from Computers & Structures Inc (the manufacturer) can answe