The letter scene that follows this is very popular, but for me this scene in S4's "The Storm" is one of the best. Sarah Slean's "Blue Parade" provides a haunting backdrop.
A video dedicated to the 6-episode S4 arc when Ben finds out that Felicity cheated on him with Noel. The video follows them as they deal with broken trust, bitterness and in the end ... love. The music chosen is Sarah Slean's "Blue Parade" due to it's excellent use in the pivotal episode in this arc, "The Storm".
In S2 of "Felicity", Ben interrupts Felicity's date with Greg and lays it all on the line. He gives her the big speech and the two of them have this angsty fight before her date punches him. It's a great scene. He doesn't get the girl here, but he does eventually and in large part cause he went out on the line emotionally in this scene.
Finally, the top two angsty moments in the Pacey & Joey relationship. While many would probably have what I listed as #2 on top, for those that know me (Sharone!), you'll understand why I picked what I did for #1. :)