Several Family Guy scenes always made me uncomfortable (for various reasons) as well:
-Stewie falling down the stairs, busting his head opened, and then throwing up
-The scene where Stewie gives birth from his NOSE after making some disgusting pregnancy ray
-Peter killing a beached whale with a fork lift
-The cutaway scene where Peter brutally stabs Yogi Bear right in front of
Boo-Boo
-The entirety of the episode Herpe, the Love Sore (except for the Electric Mayhem cutaway, I loved that of course
)
-Peter (as the woodcutter from Little Red Riding Hood) sawing Brian (as the Big Bad Wolf) in half in a very graphic fashion
-Stewie singing You Needed Me by Anne Murray to Brian (Not because it's gross or offensive, actually the complete opposite. The scene always made me cry due to how a normally silly episode suddenly transitions into a sad story about a puppy being taken away from his family. Puppy Brian snuggling up to his mother gets to me every time)
-Brian talking to Stewie about how he's always wanted to kill himself when they are a stuck in a vault together (Again, it was a very unexpected tragic scene)
-Liam Neeson's intentionally offbeat cutaway about a soldier dying in the Civil War
-The episode where Jason Voorhees shows up during a cutaway joke and repeatedly gets stabbed by his own son