I believe that luckily in most TV shows you could get chemistry like Nic/Conrad or Jack/Emily or something similar. However Ephram/Amy is on another level. It's special. It's when it's not just the actors playing the role, but they also get along in real life as people. It's something special that you don't always have.

The other case when such things happen is when you have method actors and I believe both Eimly and Greg are. By method actors I mean that they have strategy on how to play the role. Let me give you some examples. I know that in Roswell Jason would do things that are not in the script. He would be like how would I act in such scene with my girlfriend and he would put a hand on Shiri's arm or something like that because this is how he would act as a boyfriend with his girlfriend. Never mind that his girlfriend at the tame was Katherine Heigl and not Shiri.

In the same way Jesse (Chicago PD) has said that he would create in his mind backstory on his story with Lindsay. Every time they would have a group scene or scene just the two of them together he would check the overall tone of the scene. If the scene is not dramatic in the sense that they are about to arrest someone or to fight or someone's life is in danger he would physically do stuff (flirting, playing around, joking around, winking etc) to play out the closeness.

I believe that both Greg and Emily did the same in Everwood. I believe that they added their own tidbits to the scenes they had to play which is why it was so authentic, so real, so natural. They would not just act what was written on the pages, they would create their own story, they would add their own elements to the story to make it more natural. And it did make it so natural. You basically would forget that they are playing and that it's just acting.