A friend of Jen repeatedly tells her that Jack's homosexuality is a sin and she shouldn't be friends with him, which annoys Jen to no end. Then the so-called friend asks Jen's religious grandmother for her opinion. Both him and Jen obviously think she will say the Bible disapproves homosexuality or something like that, but she just says only God has the right to judge Jack, or him, or anybody. The atheist Jen is pleased.
Abby's mother asks Andie to say something nice about Abby at her burial. Andie doesn't dare refuse because Abby's mom is a nice person but she just doesn't know what to say because Abby was, well, Abby. She doesn’t want to lie either. Finally, she says that Abby's "challenging personality" made her stronger.
Jen moving back in with Grams at the end of the second season, and bringing Jack (whose barely-there father had virtually disowned him over his sexuality) to live with them.
Whole chunks of the finale. But especially Doug kissing Jack in public to make it clear that he will be there for Jack and baby Amy.
Season 3 had its moments: Pacey going out of his way to help Joey (with the B&B, the wall, etc, Jen being there (as a friend) for everyone involved in that love triangle...