The ponies’ countries are based on the similarity between looks/personalities compared to the country’s respective cultures, their economies or current situations, relations between countries, their histories, size compared to importance, or are just randomly thrown in.
 
No offence intended.
 
Here’s the list:  
Afghanistan - Diamond Tiara  
Albania - Night Glider  
Algeria - Sapphire Shores  
Andorra - North Pole  
Angola - Shining Armor  
Argentina - Button Mash  
Armenia - Thunderlane  
Australia - Braeburn  
Austria - Octavia Melody  
Azerbaijan - Flitter  
Bahamas - Winona  
Bahrain - Doctor Horse  
Bangladesh - Apple Bottom  
Barbados - Tropical Spring  
Belarus - Silver Shill  
Belgium - Mr. Cake  
Belize - Nightjar  
Benin - Sonata Dusk  
Bhutan - Wild Fire  
Bolivia - Royal Guard  
Bosnia and Herzegovina - Whiplash  
Botswana - Sew n’ Sow  
Brazil - Pinkie Pie  
Brunei - Stinkin’ Rich  
Bulgaria - Snips  
Burkina Faso - Rumble  
Burundi - Crystal Arrow  
Cambodia - Sunset Shimmer  
Cameroon - Mulia Mild  
Canada - Big MacIntosh  
Central African Republic - Igneous Rock  
Chad - Limestone Pie  
Chile - Starry Eye  
China - Twilight Sparkle  
Colombia - Sheriff Silverstar  
Congo - Flurry  
Congo (Zaire) - Soot Stain  
Costa Rica - Cheese Sandwich  
Cote de Ivore - Chocolate Sun  
Croatia - Berry Punch  
Cuba - Party Favor  
Cyprus - Sunshower  
Czech Republic - Apple Strudel  
Denmark - Maud Pie  
Djibouti - Stellar Eclipse  
Dominican Republic - Junebug  
East Timor - Pumpkin Pie  
Ecuador - Tank  
Egypt - Babs Seed  
El Salvador - Zipporwhill  
Equatoral Guinea - Bags Valet  
Eritrea - Featherweight  
Estonia - Diamond Mint  
Ethiopia - Cloud Quartz  
Fiji - Lucy Packard  
Finland - Cheerilee  
France - Rarity  
Gabon - Mane Goodall  
Gambia - Cranky Doodle Donkey  
Georgia - Cloudchaser  
Germany - Photo Finish  
Ghana - Adagio Dazzle  
Greece - Fancy Pants  
Guatemala - Ms. Peachbottom  
Guinea - Hayseed Turnip Truck  
Guinea Bissau - Sassaflash  
Guayana - Cherry Jubilee  
Haiti - Sightseer  
Honduras - Caramel Apples  
Hong Kong - Spike  
Hungary - Apreggio  
Iceland - Mayor Mare  
India - Scootaloo  
Indonesia - Daring Do  
Iran - Flim  
Iraq - Flam  
Ireland - Time Keeper  
Israel - Applebloom  
Italy - Sweetie Belle  
Jamaica - Tree Hugger  
Japan - Rainbow Dash  
Jordan - Dinky Doo  
Kazakhstan - Pipsqueak  
Kenya - Zecora  
Kosovo - Coco Pummel  
Kuwait - Pearly White  
Kyrgyzstan - Manerick  
Laos - Score  
Latvia - Dolphin Dream  
Lebanon - Dumbbell  
Lesotho - Derpy Hooves  
Liberia - Apple Cider  
Libya - Discord  
Liechtenstein - Double Diamond  
Lithuania - Lyra  
Luxembroug - Donut Joe  
Macedonia - Sugar Belle  
Madagascar - Apple Leafs  
Malawi - Riverdance  
Malaysia - Gilda  
Maldives - Skyra  
Mali - Cherry Berry  
Malta - Screwball  
Mauritania - Kyrippos II  
Mexico - Apple Fritter  
Micronesia - Rainy Feather  
Moldovia - Neon Lights  
Monaco - Hoity Toity  
Mongolia - Flash Sentry  
Montenegro - Sunshower Raindrops  
Morocco - Starswirl the Bearded  
Mozambique - Diamond Dogs  
Myanmar - Lily  
Namibia - Bulk Biceps  
Nauru - Owlowiscious  
Nepal - Lucky Clover  
The Netherlands - Granny Smith  
New Zealand - Little Strongheart  
Nicaragua - Caramel  
Niger - Marble Pie  
Nigeria - Surprise  
North Korea - Trixie  
Norway - Aloe  
Oman - Queen Chrysalis  
Pakistan - Silver Spoon  
Panama - Roseluck  
Papua New Guinea - Wheat Grass  
Paraguay - Amethyst Star  
Peru - Trouble Shoes  
The Phillipines - Red Gala  
Poland - Bon Bon  
Portugal - Fleur dis Lee  
Qatar - Filthy Rich  
Romania - Snails  
Russia - Luna  
Rwanda - Angel Bunny  
Samoa - Rivet  
San Marino - Mr. Waddle  
Saudi Arabia - Haakim  
Senegal - Matilda  
Serbia - Suri Polomare  
Sierra Leone - Manticore  
Singapore - Iron Will  
Slovakia - Mrs. Cake  
Slovenia - Minuette  
Somalia - Hoops  
South Africa - Cadence  
South Korea - Vinyl Scratch  
South Sudan - Pound Cake  
Spain - Prince Blueblood  
Sri Lanka - Tealove  
Sudan - Blue Nile  
Suriname - Truffle  
Swaziland - Red June  
Sweden - Lotus Blossom  
Switzerland - Nurse Redheart  
Syria - Trenderhoof  
Taiwan - Starlight Glimmer  
Tajikistan - Fluffy Puff  
Tanzania - Amber Waves  
Thailand - Soarin’  
Togo - Aria Blaze  
Tonga - Sweet Pop  
Tunisia - Opalescense  
Turkey - Twist  
Turkmenistan - Cream Puff  
Uganda - Gummy  
Ukraine - Golden Harvest  
United Arab Emirates - Amira  
United Kingdom - Celestia  
United States - Applejack  
Uruguay - Ms. Harshwhinny  
Uzbekistan - Dry Wheat  
Vatican City - Fluttershy  
Venezuela - Banana Fluff  
Vietnam - Spitfire  
Western Sahara - Lightning Dust  
Yemen - King Sombra  
Zambia - Esmerelda  
Zimbabwe - Pokey Oaks