There are a fair few made for the original DS, I have fond memories of Nightmare Troubadour, but it's pretty bare bones. Might scratch the itch you're looking for if you want original Yu-Gi-Oh.
For GX the first one is Spirit Caller and then they all become the World Championship games from 2008 - 2011. They evolve pretty significantly over time as Spirit Callerhas a simple world map with 2D sprites while 2009 and later have 3D graphics with better AI and decks as the years go on.
2008 is the end of the GX era and has pretty much all cards from that time. 2009-2011 cover the 5Ds era. Beyond that there's Zexal World Duel Carnival but that was the last game for a while. There are also the Tag Force games for PSP but a lot of them never got released in English and fan translations of those can be... iffy.
If you just want a story mode that's a purely linear retelling of the anime, Legacy of the Duelist allows you to play through the onscreen show duels.