There are so many good ones but I have to go back to one of the earliest books that I read because it made such an impression on me and made me want to read everything SEP had written.
My all time favorite scene is the entire bondage dress scene in IHTBY, from the time Dan realizes how Phoebe is dressed until they make love after she tells him about her past. I like the sexual detail mixed with the emotional detail. It was very intense, especially Dan trying to figure out why he was having such mixed feelings about Phoebe.
In a more recent read, as much as I love Blue and Dean, I think my favorite from that book (NBC) is when Jack realizes that his daughter had to make a cardboard guitar to practice with and he has to leave the room to get his emotions under control. Such an innocent little scene but it gives us great insight into Jack and what kind of man he really is.
This was a fun question to think about. I could almost identify a favorite scene from each book.