I've been going through Genki I via self study and I encountered the sentence:

あなたの国では、どんあスポーツが人気がありますか。

I've never seen the particle は after で, and I'm curious as to why it appears here. How is it different from just using で alone?

The は particle denotes that the previous few words are the subject of the sentence (あなたの国で). When we translate it into English it looks the same with or without the は, but は can emphasize that we are talking about YOUR country, contrasting it from other countries.

For instance, maybe earlier in the conversation I mentioned that American football is popular in the U.S., then I say to my Japanese friend, "In YOUR country, what kind of popular sports are there?" which means I'm comparing Japan to the U.S., rather than emphasizing the sports themselves.

I see. Thanks for the help!