There are two viewpoints for this problem, the language level, and the country level.
For different languages I would preffer to have them on one domain with names like index.et.html or index.html.et for Estonian, index.lv.html or index.html.lv for Latvian and index.lt.html or index.html.lt for Lithaunian. this leaves the door open for content negotiation where your webserver serves the right page dependent on the language settings of the Browser.
For local Google searches however it might be better to have a lithaunia.example.com and latvia.example.com because these might pop up at higher locations in local searches on www.google.lt and www.google.lv if Google recognizes that each subdomain represents a website for a different country. To make this happen you probably should have different IP addresses for lithaunia.example.com and latvia.example.com, where each IP address points to a server in the targeted country. If you use a server in another country, Google will probably exclude the sites when people check the search option "sites in Latvia only" because the ".com" domain gives no clue about the targetted country.