These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Moment of Awesome: Both last star gets (what happened was they lost about thirteen stars of footage due to screwing up somewhere and had to record thirteen extra ones). The first one happened when they were racing Koopa the Quick at Tiny-Huge Island, after minutes of getting screwed over, Spike long-jumps in front of Koopa and gains victory by 2/10ths of a second. See about 10:14 in this video..
The second one involved Jay going for the star on the floating island on Tall Tall Mountain in the Prelude to Bowser episode. He gets to the part where you have to roll the log and the rest is history. See 1:00 in this video.
Jay gets one for getting better in Super Mario 64. From the first episode where he died to a rolling ball and failed to get the first star, to episode 49, where he got three stars in one episode, and some of the rerecorded episodes, where he shows a lot of progress in the game.
Also some smaller ones were from Super Mario 64, where they would jump on a railing and glide backwards and jumping into the corner of the ceiling of the staircase to the third floor.
Beetle Adventure Racing, full stop. This one is more weird because they were playing it on the actual n64 and not on an emulator.
Game-Breaking Bug: One appeared during their Let's Randomly Play of Donald Duck: Going Quackers where the game never loaded the environment after an NPC text box, meaning Spike couldn't exit out of the dialogue.
Another example was from Super Mario 64 episode 44, where Spike jumped in the water shortly after beginning a level and couldn't jump out, forcing him to restart the level.
Rooting for the Empire: Among the comments in Mario Party 3, a lot of people wanted Daisy to win. Which she didn't
Squick: This little example from the end of episode 48.
Jay: It (Lethal Weapon) has Mel Gibson and Danny Glover in it.
Spike: Your mom has Mel Gibson and Danny Glover in it.