I'm going to hopefully share a bit about my experiences with this sub-genre tomorrow ( leaving my laptop behind + want to spend time on some gaming ). For now I'll say that Super Metroid is my favorite game, edging out SOTN. I played 2 of the DS Castlevania games ( Dawn of Sorrow and Portrait Of Ruin ), but they never grabbed me the way SOTN did. I also played and enjoyed the NES Metroid, and although good brings up the rear on this short list. Never gave Outland on PS3 a decent shot. Bailed on the second boss. Pussed out tbh. I have to mention I really liked Rouge Legacy when I played it on the Vita, even though it not a true Metroidvania game.
I see the Prime games included in the thread too. I loved the original Prime, but it feels weird to include it to me. Because it's 3D I guess.