It's been a tie between REmake and RE2 for quite a long time, with one of them always being my favourite and the other the second favourite, switching places every now and then depending on my mood. But both of them have been dethroned since the release of Revelations 2, which is now my favourite. It combines all the great aspects of the older and the newer games in the series, has a great atmosphere, story and cast of characters, my favourite villain so far, tons of replayability and the much beloved Rape Mode mini-game, which I prefer over Mercenaries. Also, said mini-game allows you to play as (almost) all recurring main characters in the series, which has never been possible before. I have a few complaints which aren't all too severe, but this game has done the impossible by being even more appealing to me than the originals, and it's safe to say that it will be very hard for any future RE to dethrone this one.
Edit: Some people have made a list, so I'll share my top 5 as well:
1. Revelations 2
2. REmake or RE2
3. The other one
4. Nemesis
5. RE6 (... yes, you read that right)