While the standard Windows version has all the features to run Mario, Pokémon, and Zelda titles for regular users, the Windows debug version of NO$GBA is designed for programmers. However, as you can tell by its name, NO$GBA originally started as a Gameboy Advance emulator before the developers decided to add support for the Nintendo DS and Nintendo DSi. While its name might suggest otherwise, NO$GBA (read as No Cash GBA) offers native support for Nintendo DS and DSi.
NO$GBA: Best Nintendo DS Emulator Under Active Development