I am not a fan of the Vampire Killer remix in Castlevania Chronicles, but the real offender in that game was the remix of Wicked Child. It is, quite frankly, the worst remix I've ever heard of that particular song. The original is one of my all time favorites.
Other than that I am liking most of the music in these games, but I can't stand "Invitation of a Crazed Moon" from Portrait of Ruin. I think it has more to do with the arrangment than the actual melody though. It almost has an awful funky 70's vibe to it, especially in the beginning. Can't put my finger on it but it completely ruins it for me.