Super Metroid by far, its sound track was something to behold and its graphics were very state of the art even in 2 bit sense...
the other games vary
I do like the classic and Zero mission
I also like Metroid II though its not as good as I or III
Metroid fusion is alright but it could have been a bit better
and I did enjoy Metroid Prime...

but Nintendo seems lost with the series and it is in danger of getting "kiddied out" like Mega Man, Mario, Zelda and Sonic