I've had this mental image for a long time, I can finally share it, made with inkscape.

• rasterio: Read, write and transform raster data
• fiona: Read and write vector data
• xarray: N-D labeled arrays and datasets in Python
• shapely: Manipulation and analysis of geometric objects in the Cartesian plane
• pyproj: Performs cartographic transformations and geodetic computations
• geopandas: Spatial extension of pandas

• descartes: Plotting of spatial objects with matplotlib
• fiolum: Interactive visualization of spatial objects with leaflet

• geoalchemy2: The spatial ORM
• Django gis extension: Not represented in the overview image above, but another handy option to interact with spatial databases.

• A nice blog entry by Matthew Perry to understand the concept of affine transform
• Another blog entry presenting a detailed overview of the python geospatial stack