The latest 'Stable' build is no longer recommended as it's over 5 years old and lacks any new features. It now uses less CPU/GPU resources, and Wi-Fi is also underway. DeSmuME has had significant improvements since 2018, though new features are still in development and are only available through either nightly/dev builds. DeSmuME DeSmuME works out of the box The most developed emulators for regular DS games. Switching to OpenGL in core options may give a performance boost.
melonDS does not have custom file paths yet (all saves will be created where the rom is). (Example) While the developers of No$GBA had documented the Wi-Fi capabilities first, melonDS is the first and only emulator that's gotten as far as it has and it has been found to work reasonably well with a handful of games. Both can display the two screens in a variety of ways, but melonDS has a hybrid mode. Both can run games at a higher internal resolution (sharper 3D objects) and can open roms inside an archive (zip, rar, 7z). Has similar DS game compatibility as DeSmuME. In terms of being user-friendly, options in melonDS are more simplified. Comparisons melonDS Unlike DeSmuME, melonDS can use wifi, and has some DSi support.