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There's a complete list of WFC compatible games (Wii, NDS/i) for English regions over at Nintendo: http://www.nintendo.com/consumer/gameslist/en/games-wifi.jsp
In addition, Wikipedia contains an outdated list of WFC compatible games from different regions: http://en.wikipedia.org/wiki/List_of_Nintendo_DS_Wi-Fi_Connection_games
It's safe to assume that the overwhelming majority of games are now compatible with the server - feel free to report any issues discovered with specific titles as they arise.