I love this episode -- this, along with Five by Five (I count them as a single episode, since they go so well together) is my favorite episode of both series. I've got a bunch of thoughts that are coming to me relatively randomly.
Something that I notice in it that is throughout the series: Buffy is very self-centered. Why does she track down Faith? Because she took her body and slept with Riley. Not because of anything that Faith does to everyone else (and she's done a lot), but because of what she did to Buffy. Just an interesting thing to think about (I still love Buffy, it's just a character flaw to make sure to keep in mind).
You see how much Wesley actually trusts Angel -- he sides with him and helps Faith escape from the Council, even though less than a day ago she was brutally torturing him. For some reason, the fact that he tells her to grab her coat really sticks out in my mind -- I guess because it's so odd that he's kind of looking out for her well-being.
Buffy delivers one of my favorite lines to Angel here: "So you decided to punish her with a severe cuddling?"
The "microwave speech" is one of the most Whedon-y things I can think of -- the fact that this episode was written (mostly) by Tim Minear tells me how much those two think alike. And the punchline is something I saw coming a mile away, but the fact that you knew it was coming made it work.
This episode also has the biggest gut punch line in either series:
Faith: "Buffy, I'm sor --"
Buffy: "Apologize to me and I will beat you to death."
Faith (very quietly): "Go ahead."
One thing that really sticks out to me is when Buffy and Faith are on the roof. As soon as the Watchers open fire, Buffy throws Faith to the ground to protect her, even though she just threatened to beat her to death. That's part of why I find their relationship to be so complicated and interesting.
And Faith ultimately chooses to go to prison for what she did (and, as we learn later, she's only there because she wants to be), showing how she really feels about what she's done.
And that's all that's come to mind about this episode. There's probably more, but that's all I can think of.