I use handheld/retro-v2 as my default for DS games that are fine to play while displaying a single screen (with screen switch remapped to left trigger). I use simpletex for older handhelds, but DS looks a bit strange to me with that colored paper look. retro-v2’s grid seems a bit closer to how my DS Lite looked. For games where you need to see both screens at once, like Sonic Rush, I use an interpolation shader (bandlimit-pixel).
Desmume is the most usable DS core right now since it has so many options. But melonDS has less visual glitches and better sound quality. It’s only missing a screen switch retropad button, analog stick touchscreen cursor control and cursor hide support to keep me from switching to it yet.