The abandoned Mardi Gras float that Carface, Charlie, Itchy, and the rest of Carface's gang use as a hideout, which more than resembles a huge, skeletal demon.
The vivid depiction of Fire and Brimstone Hell from Charlie's nightmare, forever putting the fear of divine punishment and existential dread into god-fearing children. Charlie imagines that his pocket watch has stopped, thereby ending his borrowed time, as he hears the Heavenly Whippet's voice echo "You can never come back." Suddenly, his watch explodes and he's sucked into a storm of green lightning towards a vortex, where a tornado bursts from the ground and pulls him down into a lava pit onto a ship made of bones that's sinking into the river. He's met by a hideous rat/bat skeleton hybrid who roars at him as he tries to get away onto the ship's bow, only for a gigantic Hell Hound to burst flaming out of the bubbling lava in front of him with a dinosaur-like roar, then send several imps after Charlie to torment him as his ship sinks further and further into the lava. The last thing he hears before waking up is the monster bellowing with the Voice of the Legion "YOU CANNEVERGO BACK!! There's a little Nightmare Retardant when the imps turn out to be Flo's puppies trying to wake him up.
The uncut version cranks it Up to Eleven and yanks the knob off. Not only do we get an unsettling close up of the boat monster, but the Hell Hound slinks down to Charlie and bellows in his face "Now, you are MINE!" Is it any surprise that this was cut for being too scary for children?
Charlie returning to Anne Marie, at least at first. A giant fiery figure, strongly implied to be Lucifer himself, looms over the town in the distance, turning the sky red as blood-red smoke billows through the streets. The smoke pours into Anne Marie's open window and for a second, it looks as if the devil is coming for her (it's just Charlie's ghost floating in). The implication is that Charlie has either come back from hell or was in limbo and the devil was coming for him.
The absolute gun-wrenching tension of watching Charlie's pocket watch at the bottom of the river filing up with water, knowing that one of those ticks is going to be it's last. After being forced to choose between saving Anne Marie and letting his watch sink, Charlie ultimately chooses Anne Marie, putting her on some driftwood and pushing her out of the burning boat to safety, all as we keep cutting back to the watch at the bottom of the river. The second we see it filling with water and ticking irregularly, Charlie winces in pain, then dives down as fast as he can to get it. We cut back to the watch one last time... just in time to see it stop. Cue the whole frame getting obscured by inky black bubbles.
Charlie's murder. Especially terrifying in that to him, everything is perfectly fine: he's out of jail, everyone's happy to see him and he's off to start his own business with half of his partner's profits. He then goes out to celebrate with his friends and gets so drunk that he can't tell that he's being lead to a trap or that his best friend is screaming at you to warn you until it's too late. And the whole thing happens so fast that it actually feels like you've been hit by a car! Charlie doesn't even realize something's up for a few minutes until he's told point-blank that he died.
Oddly enough, heaven is like this too. Part of it is the Mood Whiplash from a deep, frighting crime related death scene of the main character to a fluffy sugar bowl based afterlife, the strangely calming music and the overly nice and law-abiding dog angel. And this is just a tiny part of it that we see. It all seems too perfect (which is why Charlie immediately hates it), and it is, because there's a catch: you can either spend eternity stuck in this boring, sweet place or being damned to hell for trying to go back to earth (which many people/dogs who died unexpectedly most likely did).
Itchy getting jumped and almost killed by Carface and his lackeys, who later burn down the casino. The scene makes it clear that, for the rest of the movie, these guys are not playing around.
Itchy is so traumatized by Charlie's death at the beginning that he cries for Charlie in his sleep. Then we hear the door to their home open and see a shadow approaching Itchy's sleeping place. It turns out to be Carface, who begins strangling Itchy in his sleep as Itchy begins screaming for help. Thankfully, it's only a nightmare. Charlie was just shaking him awake.
Upon returning to life, Charlie drags himself up from the water, gasping and frantic and a sickly grey color. It takes his life watch a good ten seconds to start ticking, and only then does his color change back and his ability to breathe return. He was basically a living corpse. If you look closely, you can even see his spine reforming.
In "The Perfect Dog", Charlie becomes a sickeningly sweet "perfect dog" towards Sasha, so that he can mess with her and prove her wrong about wanting one in the first place. When she finds out, Sasha has a rather unnerving breakdown, paired with an Evil Laugh and punctuated by some kind of deranged roar.
Carface's vision of his fate in An All Dogs Christmas Carol, despite being (or rather because it is) a catchy gospel number.