Oh man, there were many cutscenes that were too good. It's kind of hard to choose which one exactly, but I'll mention the ones that got my attention the most.
"The Story So Far" - This was a neat and fun way to recap the story of the other two games. The way Qwark was narrating in an interview kind of setting was really cool and entertaining overall. It would of been a lot cooler if there were bonus videos of the other Ratchet and Clank characters doing an interview just for kicks and giggles in this game. 
"All the Time in the Universe" - This scene I liked because this is the scene where we get to ponder the most. What was Nefarious' purpose to trick the Zonies? Or How was Clank was created in a place like the Great Clock? My favorite moment was when Clank stopped and looked around at the Great Clock, it played the European time bells in the background. Those sounds made me felt a bit nostalgia inside. 
"The Junior Caretaker" - It was a nice way to introduce Sigmund in this scene, with his Kung-Fu comical gesture and replacing the screw driver that Clank was holding with a banana.
"The General and Kaden" - This moment showed a unique way to introduce Alister to Ratchet. Sure it wasn't very pleasant at first, but these two worked together later on. It's also one of those scenes that made you ponder too like "All the Time in the Universe" and it was very visually appealing with scenery and character animations overall.
"Sigmund's Secret" - I'll be honest, this is one of the scenes that made me felt quite emotional when it came to playing this game. The expressions that the characters had, the music that was played in the background and the way Sigmund sounded sad with his dialogue kind of made me felt depressed. In my opinion, it's such a powerful scene.
"The Obsidian Eye" - I really like this scene a lot because the way the animations were produced in this scene were so fluid and well done. The way the characters talked and moved were done beautifully overall.
"Five Bolts Wasted" - This was pretty much the climax. It was interesting to hear what Nefarious' purpose was to use the Great Clock for and see a clever way to destroy his arch enemy Ratchet and Clank was funnily unique. This one had some good laughs here, especially with Qwark trying to escape. 
"Alister's Folly" - There were a variety of feelings that appeared in this scene like emotional vibes, surprises and even laughter too (the way Nefarious was defeated of course) There was a moment I liked when…
After Alister strike his thunder power at Ratchet, Ratchet was breathing very heavily before he fell to his death. The use of heart-beat sounds really captured the pain and betrayal that Ratchet got from someone he could of trusted, which adds a nice touch to the scene.
"The Last Lombax" - It definitely had heart, it was pretty touching and it was a great way to end the game, but I thought there were a few things that made the scene a bit too predictable, such as…
Clank didn't want to stay in the Great Clock, Sigmund becomes the new senior caretaker, and Clank getting together with Ratchet.
Except there was one moment that surprised me quite a bit in that cutscene and that was…
Alister's death. So far, that's one of the most dramatic deaths in a Ratchet game.
I think those are my favorite for now, but I definitely like most of the scenes in A Crack in Time.
