A collection of geospatial programs with commandline interface. The starting point of the list was this tweet which contains many useful responses.

• GDAL/OGR - Powerful tools for conversion and processing of most geospatial formats.
• PROJ - Converts coordinate reference systems.
• GEOS - Performs geometric operations.
• Fiona - Process vector data.
• Rasterio - Process raster data.
• Mapshaper - Convert between Shapefile, GeoJSON, TopoJSON and CSV.
• geojsonio - Display GeoJSON files in the browser.
• wellknown - Handle WKT (well known text) geometries.
• QGIS/qgis_process - Interface for accessing QGIS processing tools.
• GRASS - Execute GRASS algorithms.
• SAGA GIS - Execute SAGA GIS algorithms.
• Whitebox Tools - Execute Whitebox Tools algorithms.
• osmium - Powertool for any type of OpenStreeMap data processing.
• osm2pgsql - Load OpenStreetMap data in a PostgreSQL/PostGIS Database. Written in C++.
• Imposm - Load OpenStreetMap data in a PostgreSQL/PostGIS Database. Written in Go.
• GeoStyler - Conversion from and to various geospatal style formats.
• Orfeo ToolBox A toolbox for remote sensing.
• shp2pgsql / pgsql2shp / shpdump Shapefile related tools.
• spatialite - A SQLite bases database for spatial data.
• topojson - Handling the TopoJSON format.
• geojsonhint - Validate GeoJSON files.
• carto - Edit CartCSS styles.
• pygeometa - Create geospatial metadata.
• osmctools - Convert, filter and update OpenStreetMap data files.
  • osmconvert
  • osmfilter
  • osmupdate
• MDAL - Mesh Data Abstraction Library.
• PDAL - Point Data Abstraction Library.
• LAStools - Tools for processing point clouds.
• OPALS - Processing of airborn laser scanning.
• CloudCompare - Tools for processing point clouds.
• OpenDroneMap - Process drone imagery.
• PCRaster
• BareMaps
• libtiff) - TIFF Library and Utilities.
• d3-geo
• d3-geo-projection
• ndjson
• go-spatial
• GMT
• mapnik - Mapping Toolkit.
• TauDEM - a suite of Digital Elevation Model (DEM) tools.
• Mapproxy - Proxy for geospatial data.
• t-Rex - Creation and Serving of vector tiles.
• Cesium Terrain Builder
• tippecanoe - Build vector tiles.
• GeoWave
• Apache Sedona
• PkTools
• geojson-merge
• felicette - Download satellite images.
• valhalla - Routing Engine.
• mbgl-renderer
• osmtogeojson - Convert OpenStreetMap XML to GeoJSON.

• Command-Line Cartography - Blog Post Series of Mike Bostock
• GeoJSON
• Vector Tiles
• Fiona/Rasterio Cheatsheet
• Talk: Are be going back to Command Line GIS
• Slides: Command-Line Geography