really good and difficult question.... let me think
mausoleum of the giants is maybe my favourite area but not a lot of individual rooms stand out to me, i like it because of the overall story it tells. i guess the one where the giant falls on you is funny
i like the really fucked up platforming rooms. the one in gate of illusion where you fight a bat over tiny half tile platforms or something. the one in dimensional corridor where like you have to time stop a jar in midair??
the block puzzle room in inferno cavern is also classic.... oh also the chain whip room where you can fuck up and softlock yourself out of getting it
does the secret tokimeki memorial section in the freeware version count. the legendary tree....
i like the three medicines room in hell temple just for the feeling of getting there and being like "i have to do this two more times, huh"
i can't choose just one room.... sorry