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.
Around the time Super Mario 64 first came out, there was a Got Milk? commercial that showed Mario in Wet-Dry World, having trouble jumping, whereupon he hops out, drinks some milk, grows extremely large, and then hops back into the level, plowing through everything in sight. Almost 10 years later, you can now kinda do it for real.
Memetic Molester: From the DS version we have Wario's character selection screen ... which shows his face with a rather creepy grin and underneath him are the words "Touch Me". Granted all the characters have the same interface, but it's the creepy grin that really drives it home for Wario.
There's also that creepy calliope music that plays in the basement of that level. The first time falling into the basement can be a fright because of it. It turns into Nightmare Retardant when you find its source, though.
After Bowser's sub-marine leaves, a huge black hole is shown on the wall. If you get too close, it will suck you in and there's nothing you can do about it. It leads you outside Peach's Castle, but it can creep you out in the first run.
No mention of the DS Port's King Boo level? Aka the one that couples both the creepy calliope music and the Big Boo's Haunt music with an absurdly chilling laughter as you venture a Lost Woods-like maze level?
The sight of Mario drowning in the original version, because of how realistic it is. The DS version makes it more cartoony.
Perhaps owing to being the first major three-dimensional platformer of the franchise, the game has some pretty terrifying drops. If you're acrophobic, do NOT play Rainbow Ride.
Polished Port: The DS Port had a better camera system, improved graphics (On a portable, no less), and added Wario, Yoshi and Luigi as playable characters. However, the controls were not as good.
So Cool It's Awesome: Super Mario 64 is viewed as the first truly good 3D game, is in the top ten on Game Rankings, and is widely considered one of the great classics among video games.