This is something that occasionally comes up when talking to clients about Globalization/Localization planning. Here is a list of best practices based on research.

1. Don’t use flags when the intent is to signal language.
2. It’s ok to use flags to represent country/market but follow with the language. 
3. Always use the name of the language in its local format.
4. Have a consistent place for the language/market selector across the site (header, footer). 

Additional Articles for Reference 

http://flagsarenotlanguages.com/blog/why-flags-do-not-represent-language

http://www.nngroup.com/articles/flag-problems/

http://www.456bereastreet.com/archive/200604/indicating_language_choice_...

http://wplang.org/never-use-flags-language-selection/

https://www.thirdandgrove.com/should-you-use-flags-for-your-country-lang...

http://responsivenews.co.uk/post/123104512468/13-tips-for-making-respons...