Haven't read about half of the thread, but I'll say that for me personally, MGS3:S topped RE4 also. However, I didn't play too many titles during the PS1 era, and have not played any other RE game except part 4 (except for a little bit of REmake), so although I can definitely appreciate how awesome of a title RE4 is in and of itself, I can't make the evolutionary comparisons to past REs like a lot of you guys can.
I have been playing Metal Gear since the very beginning, and I had really high expectations for MGS3, and they were honestly exceeded. It's in the very top tier for me.
I thought RE4 was brilliant, but I liked MGS3 more. Huge kudos to both titles.