Silent Hill is strongest in story and horror. Resident Evil is strongest in gameplay. I really liked the RE story up until Code Veronica X, meaning that I didn't really like Wesker's comeback, since I don't like it when people milk the cow so much that they revive a dead character. RE 1, 2 and 3 was great though.

It's hard to choose really, if you asked me my favorite game overall, I'd have to say Silent Hill, but if you asked me what game I'd rather replay, I'd have to say Resident Evil. Gameplay > Story, when it comes to replaying.