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.
What about you?
Super Metroid is my favorite game period, so definitely that one. Dread was really good too though, I played through that one a bunch.