The Doomsday Zone, setting the standard for final Super Sonic confrontations throughout the series. It's challenging, has great controls despite an Unexpected Gameplay Change, great music, and is a great reward for having completed all the special stages.
Mecha Sonic in Sky Sanctuary. First you fight him in two Egg Mobile bosses from the previous two games, then you fight him straight-on. Even though he's arguably easier than the Mecha Sonic in the previous game's Death Egg Zone, he has a much greater variety in movement, and you actually get to bounce backwards from Spin Dashing into him, giving a lot of options with fighting him and generally making the fight that much more exciting.
Sure, it's pretty awesome when you fight him as Sonic, but Mecha Sonic really kicks it up a notch as he's the final boss in Knuckles story. At first he uses pretty much the same tactics as when you fought him as Sonic, but then he gets right back, up and uses the Master Emerald to transform into Super Mecha Sonic. That's right, you don't just fight a simple Sonic clone robot but a character (and a villain to boot) using a Super form. His attacks in the first phase include trying to do a super roll spin to hit you from above as well as trying to shoot laser ball shots from his chest, and there's no way to harm him while he's invincible so you have to wait until he runs out of power to attack him as he keeps returning to use the Master Emerald to recharge his super form. As you get to the last phase, Mecha Sonic shoots out harmful rings in an attempt to damage you while hovering around as he loses power and gains it in midair. After two or three more hits, he explodes and the entire Sky Sanctuary collapses, and if you managed to get all of any sets of the emeralds, Super/Hyper Knuckles appears safely on the wing of the Tornado with Sonic, giving the hedgehog a thumbs up and smile as the Master Emerald is taken back to the Floating Island and it raises almost out of the atmosphere. If Knuckles had not yet proven he was worthy of being called a badass, he certainly was after a final boss like that.
The IceCap Zone theme seems to be particularly popular, remixed so many times on OverClocked ReMix that it became a meme, resulting in an April Fools album consisting of nothing but new IceCap mixes.
The soundtrack also got additional respect once word got out that Michael Jackson's sound crew partially composed it. Many parts of each song are either heavily sampled from or inspired by his Dangerous album and standalone tracks.
Though not technically part of the soundtrack, the Right Said Fred (yes, the I'm Too Sexy For My Shirt guys) song Wonderman contains several references to the game and the music video is essentially a musical ad for the game. In the UK, it was a good chunk of the game's advertising.
The PC compilation, Sonic & Knuckles Collection, had tracks in the second half of Sonic 3 that were exclusive to that game and never present on the Genesis version or any re-release afterward. Which is a shame because some would consider those tracks even better than their Genesis counterparts.
The favorite among fans is IceCap Zone, which is quite fast-paced even for this game and has one of the biggest fan favorite music tracks of the series. It was probably the most requested level from Sonic 3 for Generations, and was, to the disappointment of many, not included in the game, and neither did any level from the Sonic 3 half for that matter. It wasn't completely forgotten, as its modern re-imagining in Sonic Adventure can attest to. Sonic even gets to ride a snowboard again (this time up against an avalanche), and Tails can get in on the action as well.
Hydrocity Zone. It's an underwater ruins level, so if you've played the previous games, you're expecting a hard, long slog, right? You'd be wrong. It's a blitzing-fast wild water ride with Sonic blazing across the surface of the water, bouncing everywhere with the Water Shield, rolling down hills at ludicrous speed, getting caught in currents that fling you miles into the air, and AMAZING music.
On the Sonic & Knuckles half:
Lava Reef Zone. Seeing the Death Egg stuck in the ceiling of the massive cavern and watching as the entire lava-filled cave suddenly turns to crystal is breathtaking, and the songs for both acts go along with it perfectly.
Sky Sanctuary is breathtaking. The fact that it's nearly impossible to die on the stage makes it very easy to speedily run through the straightaways, with excellent platforming to boot. Also, it contains the boss fights against Mecha Sonic. It gets even better in Sonic Generations, just without Mecha Sonic.
Breather Boss: Knuckles. He's ridiculously easy to beat, but even so it's still satisfying to finally get revenge for all of the cheap tricks he's pulled since the start of the game.
Breather Level: Hidden Palace Zone. Mushroom Hill is also this if you lock on both games, as it's the first level of Sonic & Knuckles. It's quite easy and is shorter than most of the levels in both games. IceCap is also notable because it's quite short, but has difficult bosses.
If you're playing as Knuckles, Carnival Night Zone is a joke. The first act is quite a bit shorter than if you're playing as Sonic and/or Tails, and the second act isn't even half as long as it is then. No Barrel of Doom or even a boss for you to fight; you can literally blitz through it in around 2-3 minutes.
Contested Sequel: The & Knuckles half. Some consider it a worthy expansion to the Sonic 3 half, while others consider it a slow, inferior, rushed addition.
The whole game itself is this to Sonic 2. Both sides argue whether their game was the best 2D Sonic game and which one had the better level design.
Cult Classic: Compared to its other Genesis predecessors, Sonic 3 & Knuckles doesn't have as much mainstream public recognition due to a number of factors. The game didn't sell nearly as well as its predecessors (neither half a pack-in title like its predecessors, to be fair) and when it was released the Sega Saturn was already announced and nearing release. Despite this, Sonic 3 & Knuckles is very well-loved within the core fandom and is a common contender for best game for the franchise.
Chainspikes, the blue enemies in Death Egg Zone with four spikes. You need to hit them from a diagonal angle (easier said than done) or else the spikes positioned in four directions will get you.
Orbinauts, black orbs with four spiked balls orbiting their body, returning from the original Sonic the Hedgehog in the Launch Base Zone. Unlike their ice counterparts in the previous level, Orbinauts are smart enough to keep the spiked balls instead of throwing them out and leaving themselves defenceless.
While it is possible to defeat Chainspikes and Orbinauts as Sonic without taking damage through the careful utilization of the Insta-Shield, poor Tails cannot defeat these guys without either conventional or mercy invincibility.
Skorps, the brown mechanical enemies in Sandopolis Zone that attack by trying to sting you with their spiked tail. Their attack is almost impossible to dodge, and if you do somehow dodge it, you'll have to watch that it doesn't hit you when the tail comes back.
Ensemble Darkhorse: Mecha Sonic, to the point that some of his fans actually prefer him to Metal Sonic, the more prominent robotic Sonic knockoff.
Fandom Berserk Button: Saying that Sonic & Knuckles should have been called Sonic 4, or any implication that Sonic 3 and Sonic & Knuckles are two separate games.
Sonic Adventure didn't have Super Sonic because they couldn't figure out how to pull it off (there's even a hidden message with Tikal explaining how to turn Super). Of course, there's been many games since then that they could have spent trying to figure out how to pull off Super Mode in ordinary gameplay. They finally succeeded in Sonic Colors. They brought it back for Sonic the Hedgehog 4.
The Hyper Modes are quite powerful, but the Bonus Stages make them true game breakers. In Sonic 2, Super Sonic was more balanced since every level had a finite number of rings and hence a hard time cap on how long you could stay super. But in Sonic 3 & Knuckles, the Glowing Spheres Bonus Stage allows you to earn oodles of rings with relative ease when you know how to play it; specifically, the Ring bubbles can give anywhere from five to three-digit numbers of rings, allowing for a risk-free (unlike the slot machine) way of grinding for rings. You can also manipulate the system because the Bonus Stage you go to at a Starpost is determined not randomly, but by how many rings you're carrying. By playing only the Glowing Spheres bonus stage at each Starpost, it's possible to finish every Act with 999 rings, which are worth 999 seconds of Super transformation time. That's over 16 minutes, and the game's timer allows you only 10 minutes per act.
The Insta-Shield (which attacks enemies while protecting Sonic, and can be used anytime without a proper shield) and the Lightning Shield (which doubles Sonic's jumping height) make most bosses a cakewalk. For instance, when facing the Launch Base Zone Act 2 boss (which is one of the final bosses in the standalone Sonic 3), instead of facing Robotnik properly, you can double jump up to his "nest" area prior to the boss battle, and defeat him literally before the battle even begins.
Having a second player play as Tails in Sonic & Tails mode can easily dispatch most enemies and bosses, since Tails can't lose rings when hit.
In the boss battle for Angel Island Zone Act 2, you are completely immune to the boss' attack if you're equipped with a Flame Shield.
Skorp, the scorpion in Sandopolis Zone. Touching the spiked ball on its tail get the player character hurt, and it will also use the tail and try to attack Sonic at an aimed angle. And it's very accurate.
Same goes for the ghosts in Act 2 of the same zone, especially when it is dark— they grow big and attack in numbers, and they can't be killed off permanently.
Blastoid can be a bit of a goddamned bat in Hydrocity Zone. Especially since he will inevitably hit you at least three times throughout the level. Most likely even more, considering his placement.
Batbot can be a literal Goddamned bat in Carnival Night, as it follows you forever and therefore can end up in some inconvenient places, knocking you back.
The points from destroying successive robots or bricks went 100, 200, 500, 1000, and stays at 1000. But there is a mechanic left over from the original Sonic the Hedgehog: upon destroying the 13th object, the score jumps to 10,000. There is only one area in the original game this can be done (you can destroy 16 blocks in a row if you do it right), but there's also one in Sonic the Hedgehog 3: in Launch Base Zone, right near the beginning, there's an alarm that summons a flying robot. Doing a Spin Dash in that alarm and staying there to keep setting off the alarm will summon robot after robot, which fly right into Sonic and are destroyed. Since you get an extra life every 50,000 points, it's possible to rack up over 200 lives until either the life counter or score maxes out.)
In Sonic 3 by itself, through some stage select hijinks, you can get the game to play music from the wrong stage.
Have you ever wanted to hear the Sonic & Knuckles mid-boss theme while fighting a mid-boss in standalone Sonic 3? Here's how. Also, this fight plays the wrong (major boss rather than mid-boss) music to begin with...
In Launch Base Zone, there is a part of the level where Robotnik in his Eggmobile tries to fly off with a box. However, he only flies off if the player jumps up to a certain height. As such, if the player is playing as Sonic and Tails, he can use the 2P controller to control Tails and attack Robotnik. After 256 hits, Robotnik pops like a regular badnik and releases either a blue bird or a white chicken. See the video here. Now we know the real reason as to why he was called Eggman.
When ducking, you'll scroll the screen downwards. With some precise movements, it's possible to go inside the floor, possibly skipping some sections of the level.
And there are plenty more documented by YouTuber ORKAL (though not all of them are so benevolent):
In Sonic 3 alone, you can bounce with the Water Shield as Super Sonic. This got fixed in S3K however, and doesn't work with the other shields in Sonic 3 alone.
In Hydrocity Zone Act 1 for Sonic 3, if Tails died by drowning approximately one second before the message "Act 1 Completed" appeared, there's a chance he won't respawn for the rest of the next act, so good luck in defeating Robotnik by yourself. You can make him reappear by entering and then finishing a Special Stage or any Bonus Stage, however (regardless you win or not, in the case of entering Special Stage).
Hilarious in Hindsight: The excessive amount of diabolical giggling that Knuckles does throughout this game whenever he thwarts Sonic's quest becomes even funnier after the release of Sonic Adventure when his theme song insistently declares "Unlike Sonic I don't chuckle!" Yeah Knuckles, sure you don't.
HSQ: Angel Island being engulfed in flames, Sonic being nearly bombed by an airship, Eggman destroying an entire temple, Sonic snowboarding down a tall mountain, Eggman stealing the Master Emerald, and Super Sonic chasing Eggman down through space. And may we say that all this was achieved on the Sega Genesis?
Memetic Mutation: Michael Jackson's involvement with the soundtrack of Sonic 3 has inspired many a Sonic/MJ music mashup, with some...interesting results.
Adding "& Knuckles" to things like cover art of other video games or even pizza boxes with Knux photoshopped in somewhere has caught on.
To a degree, Eggman'sdiabolicaltraps. A short-hand developer's excuse in the manual for Sonic the Hedgehog 3's rushed development and buggy state.
Never Live It Down: This game is known as "the one with the stupid Carnival Night Zone barrel", and urban legends have sprung up about how SEGA's hint hotlines would would begin with automated messages on how to overcome them.
The moving wall in Hydrocity Zone Act 2, especially if you played the game as a kid.
Everything about Sandopolis Zone Act 2 is creepy. The solid thud sound those sliding doors make when they close can create a feeling of entrapment (especially with the lights off), and with a wild enough imagination, you suddenly realizewhy there are three ghosts haunting the pyramid. On top of all that, the music itself is easily the darkest of any track in the entire game.
It's especially bad when you start that act as Knuckles, since his story takes place after Sonic's one, the lights are already off, the ghosts are in the red zone and ambush you first thing when the act starts with no rings to protect you, so you need to be quick about turning that first light on when starting that part of the game as Knuckles.
Sacred Cow: Aside from a small faction that prefers the level design of Sonic 2, Sonic 3 & Knuckles is generally held as the pinnacle of perfection by the fanbase, and even lightly criticizing it is bound to get you backlash.
The Scrappy: The infamous "Barrel of Doom" in Carnival Night Zone Act 2, responsible for keeping many players from continuing if they didn't have a guide on hand or luck in finding out how to operate it.
Scrappy Mechanic: Despite the levels being between two and three times the size of what was seen in the previous Sonic games, the ten minute time limit remains. Some levels are legitimately difficult to finish without losing a life to the time limit, particularly the second acts of the Carnival Night and Sandopolis Zones.
Stop Helping Me!: Tails, when he's tagging along with Sonic. If you get a friend (or yourselfnote This is extremely easy in the PC version or via emulation) to control Tails with the second controller, he can be extremely helpful. But if the AI controls Tails, then he'll get in your way, collapse platforms that you want to use, attack enemies and bosses half a second before you do (so they'll have Mercy Invincibility by the time you hit them), and all-around make a nuisance of himself.
Suspiciously Similar Song: Specific examples are listed on the trope page, and helped spur the later-confirmed rumors that Michael Jackson and\or his team was involved in composing music for the game. Another similarity of note is Ice Cap Zone to "Hard Times" by the Jetzons, a band for which composer Brad Buxer was the keyboardist.
Marble Garden's boss can be annoying to defeat with Tails alone. While Knuckles faces a entirely different boss and Sonic can hop on Robotnik's head with no problem, Tails must carefully fly towards the lower part of his pod taking care to not hit either the drill in its front or the fire on its back, since his tails are the only part that can cause damage while flying.
Marble Garden's mini-boss can also be problematic with Knuckles. Not only does his shorter jump make it harder to reach, but the spikes platform also retracts and protrudes every second, meaning you have a shorter window to properly hit the boss while using a character that takes longer to do so.
Red Eye is that one miniboss, having two phases and can be rather tricky when trying to fight without getting hit. Other minibosses in this game tend to be easy.
Both the miniboss and main boss of IceCap Zone are considered this by some players, the former because it's hard to hit, and the latter because its freezing attacks are randomized.
The "final boss" of the Sonic 3, aka Big Arm, can be one of the most intensely frustrating fights, especially for newer players. Eggman's hurtbox is so miniscule yet it's covered on the top by spikes and on the bottom by the shoulder of the arms. AND you have to dodge the hands or else he grabs you and you take damage. And if that wasn't enough, he can even damage Super Sonic (due to a programming error; not intentional). It's likely for all stated reasons why this boss was removed for Sonic's path in the combined game (it's still there in the Knuckles path, but it's much easier thanks to Knuckles' gliding).
Carnival Night Zone Act 2. The level seems designed to waste your time, so that you'll invariably run out the timer while fighting Robotnik (unless you use Sonic's Insta-Shield against him). And it features the infamous Barrel of Doom...
Sandopolis. That level also really wastes your time, and the ghosts in Act 2 really get on your nerves after a while. And that's not even getting into the "endless, looping sand slide" part.
Death Egg Zone Act 2, the last full level for Sonic and\or Tails, has a lot of dangerous traps, an upside-down gravity gimmick, and many star posts that don't have rings near them.
That One Sidequest: Many of the Super Emerald stages in Sonic 3 & Knuckles are headaches, if only because their level design is really weird.
They Changed It, Now It Sucks: The PC port known as Sonic & Knuckles Collection bothers some players because all the music is in MIDI format (though with an FM synthesizer it sounds much closer to the original Genesis tunes), and several music tracks are outright changed, including IceCap Zone. That said, several of the new tracks can be quite good in their own right. Look them up and judge for yourself!
Visual Effects of Awesome: The game demonstrates 2D animation techniques that were unheard of for the Sixteen Bit Era. Highlights include the incredible pseudo-3D effect in the special stages, the water in the background matching up perfectly when underwater, and parallax scrolling that actually makes the backgrounds look like an actual world.