Languages:
R, Python, JavaScript, HTML, CSS
Formats:
CSV, ODS, JSON (.json, .geojson, .topojson), SHP, HTML
Tools:
GDAL - Geospatial Data Abstraction Library - a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
http://www.gdal.org/index.html
ogr2ogr - converts simple features data between file formats
http://www.gdal.org/ogr2ogr.html
Open Source Geospatial Foundation - OSGeo was created to support the collaborative development of open source geospatial software, and promote its widespread use.
http://www.osgeo.org/
QGIS - is a cross-platform free and open-source desktop geographic information system (GIS) application that provides data viewing, editing, and analysis capabilities.
http://www.qgis.org/
Mapbox - mapping platform - repos on github
https://www.mapbox.com/
Tabula is excellent for PDF scraping, however its a resource hog:
http://tabula.technology/
Scraperwiki is mentioned in another response, but sadly they've moved on to charging, however you can set up your own version from their sourcecode:
https://github.com/scraperwiki
Google Drive is great for easy storage, sharing/collaborating, and converting to/from other formats.
http://drive.google.com/
I can't emphasis how great drive is for alot of the work I do. You can even use it for scraping HTML tables into Google Spreadsheets, utilizing the importHTML
function; read more here:
https://eagereyes.org/data/scrape-tables-using-google-docs
Web Scraping with Google Docs:
https://docs.google.com/presentation/d/1HrCFCMh5XxF4JSma_A5-QpAvlyFhpeBzWkZT7CvEsS4/edit#slide=id.p
geojson.io is amazing for a number of things:
easily convert kml into geojson, topojson, csv, and shp
github/gist integrations allows for easy storage
view maps instanteously upon upload
http://geojson.io/
mapshaper also provides easy format conversion from shapefiles
http://mapshaper.org/
ogr2ogr web client - convert gis data formats
http://ogre.adc4gis.com/
leaflet.js - An Open-Source JavaScript Library for Mobile-Friendly Interactive Maps
http://leafletjs.com/
heatmap.js - Dynamic Heatmaps for the Web
http://www.patrick-wied.at/static/heatmapjs/
datahub.io for data storage/sharing
http://datahub.io/
ckan for running your own data portal
http://ckan.org/
Open Data Kit - (ODK) is an open-source suite of tools that helps organizations author, field, and manage mobile data collection solutions.
https://opendatakit.org/
data.gov - tools they use, repos on github
https://www.data.gov/developers/open-source
Open Data Tools - Tools to Explore, Publish and Share Public Datasets
http://opendata-tools.org/
Nokogiri - web scraping library (ruby)
http://www.nokogiri.org/
Mapping Cheatsheet - this list has some tools already listed, but in greater detail, as well as more tools, plus information in regards to choosing that apply to your particular data:
https://github.com/tmcw/mapmakers-cheatsheet
US Census Github Tools
https://github.com/uscensusbureau
Open Data Research Portal
http://open-data.fokus.fraunhofer.de/en/platform/
Guides:
Open Data Guide
http://opendata.guide/
Project Open Data - Open Data Policy — Managing Information as an Asset
https://project-open-data.cio.gov/