I am looking for a dataset describing (nearly) all languages, and where they are spoken.
Bonus if the areas are linked to Geonames or another mainstream geographical dataset. Polygons are also OK.
It does not need to be a 1-1 mapping, as many places have several languages.
Official languages is OK, but actual usage (more than 1% of the locality's population has it as its mother tongue) of non-official languages would be even greater.
I am looking for sub-country granularity.
The CIA Word Factbook has a field listing for languages spoken per country and percentage of population that speaks it.
https://www.cia.gov/library/publications/the-world-factbook/fields/2098.html
For finer grain, you can Google 'language spoken home dataset'. This will find census datasets related to the distribution of languages spoken. Below are some examples:
United States (Census) by state:
https://www.census.gov/hhes/socdemo/language/data/other/detailed-lang-tables.xls
City of Chicago, IL by neighborhood:
https://data.cityofchicago.org/Health-Human-Services/Census-Data-Languages-spoken-in-Chicago-2008-2012/a2fk-ec6q
City of Cambridge, MA by neighborhood:
https://data.cambridgema.gov/Neighborhood-Census-Data/2007-2011-Language-Spoken-at-Home-by-Neighborhood/sba5-5kgg
Madison County, NY
http://cnyvitals.org/madison/demographics/language-spoken-at-home/
State of Hawaii:
https://data.hawaii.gov/Culture-and-Recreation/English-ability-by-language-spoken-at-home/i9hq-hna6
Canada (from their Census) by Province, Electoral District:
http://data.gc.ca/data/en/dataset/81a2bd6e-622f-4f17-84c1-215216485992
Queensland, AU by statistical area:
https://data.qld.gov.au/dataset/language-spoken-home-sa4-qld/resource/9fa1fc3a-ab09-4c99-a60f-f95c59269492
Greater London by borough:
http://publicdata.eu/dataset/first-language-spoken-at-home-borough0e333
UNESCO Atlas of the World's Languages in Danger:
http://www.unesco.org/culture/languages-atlas/
Countries of the World Includes country language attribute for 249 countries - I believe either point or poly; has points for admin1 if you are looking subnational
Global Database of Events, Language, and Tone Uses the CAMEO taxonomy which I believe includes language but you'll have to check
The go-to site for linguists who are looking for language data (including e.g. their families, iso codes, position etc.) is glottolog.org. They have all their data available for download in several formats. wals.info is also useful, but that one uses a more restricted set of languages that might contain less sub-national languages.
Some time ago I made a csv file with ISO 3 language codes, latitude, and longitude of more than 7000 languages. The data was extracted from the RDF graph downloaded at Glottolog and sanitized (some coordinates missed a decimal point).
Example entry:
gui;Eastern Bolivian Guarani;-61.7179;-21.0909;;
You can download the file iso3_language_codes_with_geo_coordinates.csv from this Github repository.
License: http://creativecommons.org/licenses/by-sa/3.0/
Update:
I just stumbled on the "World Atlas of Language Structures" on Kaggle, containing data on the linguistic structures in 2,679 languages, including geo coordinates for each language.
Splitting this into 2 posts so I can post more than 2 links. I would look at
Languages of the world Last time I checked data was bound in a pdf but that may have changed. For each country, details of each language including the region (in prose).
Indigenous living languages from Worldmapper Primarily sourced from ethnologue. Indigeneous languages of each country as Excel file, no sub-country data.
You may want to look at the language data from Ethnologue at http://www.ethnologue.com
Two caveats:
Example in Papua New Guinea: 
