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.
Inside the volcano of Lethal Lava Land, there is the lava equivalent of a waterfall. Jumping into it will get Mario's butt burned as usual, but with some precise jumping, Mario will somehow stick to it and continue going upwards. Doing it just right can save a big part of the track upward to the star. Doing it deliberately wrong can end up catapulting Mario towards the very top of the level which looks hilarious.
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), extra missions, and added Yoshi, Luigi and Wario as playable characters. However, the controls were not as good due to the DS d-pad and touch screen not being as precise as the N64 analog stick; this issue alone ruined the game for some people.
This issue becomes moot, though, if you play the game on a 3DS, whose circle pad emulates the analog stick much more faithfully.
Seinfeld Is Unfunny: Zigzagged; the game is still universally considered a milestone of video game history and very fun to this day. But from a technical perspective, the game is really showing its age now, due to its very simplistic, low polygon models and stages, not to mention the abundant amount of exploitable glitches. And many of its once unique features (a fully controllable, free roaming 3-D character and world, with a controllable camera and analog stick controller) are considered passe now in light of its many, many imitators and modern video game blockbuster titles that constantly push 3D graphics to their limits (i.e. God of War, Grand Theft Auto), including this games' own follow-ups like Super Mario Sunshine and Super Mario Galaxy.
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.
Viewer Gender Confusion: Dorrie the sea monster. Despite having a feminine-sounding name and a cutesy appearance, Dorrie is officialy a male.
This is subverted in Mario Party 3, however; the description of one mini-game refers to Dorrie as a "she".
Many people assume Tuxie is a boy, when actually Tuxie is a girl. In fact both baby penguins are girls.
Vindicated by History: The DS remake has become this, thanks to the 3DS. On release, some hated the DS version for being unplayable thanks to the DS's lack of a control stick (although many didn't really mind the D-pad). But with the 3DS's circle pad, many have found it to be much more enjoyable and playable (despite the inability to walk by tilting the pad), thanks to it being a far more suitable alternative to a control stick.
Visual Effects of Awesome: Yeah, the visuals look very primitive and outdated now, but they were nothing short of jaw dropping for their day, and the appealing cartoon art has helped take the burden off the aging graphics, which is more than can be said for many other 3-D games of the time period. And even today, it's a fantastic use of the N64's color palette. It might not have been as sharp as stuff today, but it certainly looked nice regardless.