In respect to Google and other search engines they will determine the language based on the content. So other than having unique URLs for the different content normal site structure considerations come into play. I would also be inclined to use a subfolder and Google's webmaster guidelines for multi lingual sites show no preference.

Heres the relevant bit:

Google uses the content of the page to determine its language, but the URL itself provides human users with useful clues about the page’s content. For example, the following .ca URLs use fr as a subdomain or subdirectory to clearly indicate French content: http://example.ca/fr/vélo-de-montagne.html http://fr.example.ca/vélo-de-montagne.html

Signaling the language in the URL may also help you to discover issues with multilingual content on your site.

Hope this helps.

Is this in response to a notice from Google or general house cleaning? And you need to asses if those links are actually causing you any harm in the first place, for example are they nofollow?

First step in removing links is always to try and contact the webmaster and ask them to remove the links. this is important as this will then impact on all Search engines, not just Google which would be the case if you automatically went for Disavow tool. It also provides you an audit trail if in future you find you need to demonstrate to search engines, say through a reconsideration request, that you have made an effort to clean up your site and comply with webmaster guidelines, To find contact details for a website you can try contact details on the site itself or look them up with tools such as the whois directory.

If contact fails, or if they demand money for removal then you should consider using Googles Disavow tool. Again please note this will only impact Google's algorithm. It should only really be a last resort however. You can access this through Webmaster tools, just search for disavow tool in the help section to the top right and follow the links,