I have not seen any wine stoppers that featured different flags, but Pottery Barn has some awesome, unique wine stoppers. There are many creative people out there, maybe you can find a tutorial and make your own wine stoppers.
I have not seen any flag wine stoppers, either. If you can not find or make flag wine stoppers, maybe you can find stoppers that represent the countries. I have seen elephant wine stoppers, that could represent India or Asia.
My wife and I just begun making wine stoppers and are open to custom orders. We would be more than willing to try and make flag wine stoppers if you are interested. Please stop by the shop and have a look. Its under StyleandGrace1 on Etsy.com
Flag wine stoppers would be such a great way to individualize bottled wines. I'm surprised they aren't all that easy to locate. Good luck with your endeavor. I love that you can have special made-to-order products done fairly easily.
Have you tried ebay? You can usually find almost anything on there. The only other thing I could think of would be to find a wine supplier online and see if they have a catalog or maybe a special order from your local wine shop.
Check out Etsy, or party sites like Oriental Trading Co. This might be a fun project to try if you're into crafting. I think you might be able to find some ideas on the Martha Stewart website. I get my label ideas from her.
This would be a great idea and very festive depending on what country you live in. I could easily see American flag ones for Independence Day, Canada for their holidays and so on. Great idea I am sure you can find some!