My favourite Metroid game has got to be Zero Mission on the GBA.
A weird choice maybe but it was my first metroid when I played the GBA, I thought the music and atmosphere was kick ass and enjoyed the simple enough controls.
For a 3D Metroid it would be the trilogy on Wii at the time.
Going to use this thread to recommend AM2R which is so high quality Nintendo could have made it themselves. It also has a great Prime-style OST in a 2d game which none of the other games have done