Turnabout Storm/Tear Jerker

• Nick accusing Fluttershy of the murder to buy more time, especially Twilight's reaction and Phoenix's own.

Twilight: I-I can't believe you're saying this! I trusted you!
[Later]
Twilight: Phoenix... How could you...
Phoenix: (What have I done...?)

• • Not to mention Fluttershy's reaction. The last thing she says before being forcibly escorted out is:

Fluttershy: W-wait, where are you taking me? I wouldn't do that to anypony... Twilight, Mr. Phoenix! HELP!

• • Which becomes even more heart-wrenching if you've played the games when you remember that he's also had to accuse an extremely woobie-tastic witness during his darkest hour just so he could get more time. You can see that he's completely regreting having to do that again, and Twilight's reaction towards him just twisted the knife further.
• The way a few of the friendships among the Mane Six and also Phoenix Wright are utterly shattered in part 3. Twilight has already been covered, and now Rainbow despises Fluttershy for (albeit unknowingly) destroying any hope of her being found innocent with her testimony.