Hmm...off the top of my head, in no particular order;
After Amber dies and Wilson is thinking about leaving, House admonishes him. They're comparing physical pain to emotional pain, House's leg to Wilson losing Amber, and they're talking over one another, ending with... House - "You don't know what it's like..." Wilson - "...Neither do you."
House is interviewing for new fellows, and the "cool" guy comes in, with long hair and a tattoo, and he says to House; "I thought you'd be cool with rebellion." House dresses him down about how he's not rebelling, he's doing what everyone else does, and that the people who really don't care are the Asian kids with pocket protectors studying in the library 12 hours a day. He then admits to someone right afterward that even that's wrong...those kids are just doing it due to cultural pressures.
When House gets Wilson high on meth and Wilson does the breast exam.
Three Stories
Many, many moments with Chase. You can often see him in the background, reacting to House's jokes as if he thinks they're serious, or checking out a hot girl that walks by, or even things completely out of focus. Jesse Spencer is the master of background hilarity.