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.
I would agree with Dread. It is such a a nice clean game and that last boss was an actual challenge. Many games are awesome but fumble the last boss.
Before Dread, I would say the Super Metroid on SNES, that game introduced (at least me) the wall jumps and the sprint to down boost jump thing. I always tired to saved the animals when leaving the planet, but it's not like they were able to get off the planet, so I'm not sure if it really helped.