Here is a list of the enemies in Legend of Zelda: Minish Cap, along with some tips on how to defeat each type.
You'll find Acro-Bandits in the Lon Lon Ranch and Eastern Hills areas. You'll see one pop out from underground, and a moment later, a stack of five will pop up and start moving toward you, not unlike Pokey the cactus in Super Mario games. To have an easy time of defeating this enemy, kill the one that pops out of the ground before it has a chance to jump up with its buddies. Otherwise, when you swing your sword at the stack of them, they'll scatter and probably hit you, and you need to defeat all of them before they have a chance to burrow back in the ground, or each one will bring four more with it.
These automaton robots lie dormant until you come near, then they come to life and attack you. Or, in some cases, a dormant Armos will be blocking your path. The Minish created Armos, so you must shrink to Minish size to outsmart them. You can safely approach an Armos as a Minish; it won't awaken. Climb up the ladder-like ridges on its shield, and you'll be able to go inside of the Armos and extinguish (or, if necessary, light) the flame that gives it power.
Seen in plenty of past Zelda games, the Ball and Chain soldier swings the ball and chain in a circle, pulling it back in for a moment from time to time. That is the time to strike. The ball and chain do extensive damage to Link, so use your shield or keep your distance.
Found under pots and in cut grass, the beetle can't hurt you, but if a beetle jumps on you it will crawl on you, slowing you down and preventing you from using your weapons; not a good situation if you're surrounded by tough enemies. Press B repeatedly to make the thing jump off of you, and then use your sword to kill it.
You'll find these casually strolling in dungeons, but if you touch it, the thing will go haywire, dashing around the room at an angle until it eventually explodes. You can hit it again to destroy it. Or, perhaps the best method, hit it with a boomerang to destroy it instantly.
Floating menacingly in the air, the Bombarossa explodes when touched. If a Bombarossa is next to others, they, too, will explode if its neighbor does. This can lead to a nasty chain of explosions. Keep your distance from these bombs.
Moblins are huge monsters that walk around like humans but have a pig or boar face. Bow Moblins carry bows and arrows and will shoot at you if they have a straight shot.
These indestructible stones are constantly raining down the sides of Mt. Crenel, creating hazardous conditions for climbers. Take care not to be in the path of one of these.
Spitting at your customers is usually not a good business strategy, but the Business Scrub can't help it. Deflect a nut at the Scrub with your shield to stun it, then talk to the Scrub and he'll offer to sell you something--in some cases a valuable, one-time-only item.
Similar to a Trap, a chaser is a red, razor-sharp object that sits dormant in part of the room until Link comes near. When you approach, it reveals its blades and starts coming after you. If you get far enough away from it, it goes back to sleep again.
These grinning slimes will slither their way toward you, and all you can do is swing your sword to kill them. Watch out for the electrified blue ChuChus: you'll get zapped if you don't wait for the electricity to go away. Stunning a blue ChuChu with your boomerang will also stop the electricity for a moment.
These fanged fish float in the clouds, normally only evident by their sharp fins. Near Link, they jump up and attack--this is your chance to strike. They take two hits to kill, so take your time and be careful.
Crows are black birds that sit on trees. If you walk nearby, a crow will fly out and dive-bomb you. If you side-step the attack, swing your sword a few times at it to kill it.
Dark Nuts are big, armored soldiers that defend themselves on the front with a round shield. Their sword swings are very damaging, but you can use your shield to try to avoid the damage. You'll need to dash around the Dark Nut or attack when it pauses after a big sword swing, because you really can't hit it from the front. Other weapons work on these guys as well. Red Dark Nuts are more powerful, so be careful.
These red or pink doors look like regular doors that require a key to open, but they are actually traps. If you get close to one, the "door" will fall on you, hurting you. If you pay attention to the top of the door, you can see that it falls at a slight angle for a moment just before falling on you, giving you a chance to run out of the way. You can also use the map to see whether a door is real or not. There is no way to actually kill these trap doors; all you can do is avoid them.
Eyegore Statues do nothing but bounce toward you when you come near, threatening to crush you. To defeat an Eyegore Statue, you must shoot it in the eye with arrows. If there is a motionless Eyegore blocking your way, shoot its eye with an arrow to awaken it, then shoot it again a few times to kill it.
As with past Zelda games, the Floor Master will grab you and take you back to the entrance of the dungeon. They do not fall from the ceiling like in some Zelda games; instead, they just roam around rooms. Swing with your sword to kill them. They take a lot of sword hits to kill.
These pots look almost exactly like normal ones, but when you enter a room with them, they fly up into the air and throw themselves at you. Just use your shield to break them, or sidestep them so they won't hit you. Striking with your sword can also work.
Ghini look like one-eyed ghosts that stick out their tongues. If a Ghini catches you, it will drain your life slowly away unless you can struggle free. You can kill them with your sword.
Gibdos are mummies. They are very strong, taking a lot of damage before dying. Like Ghinis, they can grab you and drain away your life. When you swing your sword, they aren't knocked back like most enemies, making them especially tricky. You can use your lantern on them to burn away their wrappings to turn them into Stalfos, which are much easier to defeat.
Helmasaurs are little red monsters that wear a sharp, metal mask. When one sees you, it will dash toward you, hoping to jab you with the sharp mask. You can't hit it from the front, but you can defeat it from the back. To make things easier, you can also use the Gust Jar to pull their masks off, revealing that they are somewhat egg-shaped--not pointy-nosed at all. In fact, they look a little like Foppy from EarthBound. At any rate, without the mask, Helmasaurs stop dashing around, making them easy to defeat with your sword.
Keaton has a fox face (with some sort of X-shaped scar on the forehead?) and carries a small sword. When a Keaton sees you, it will dash toward you and hit you with the sword, knocking some of your rupees and other things out of your wallet.
Keese are bats. They fly around randomly and are otherwise very easy to defeat.
Just like in Super Mario Bros., Lakitu hovers around on a cloud. They don't throw down Spikies, though; instead, they shoot lightning bolts at you. They are easy to stun with the boomerang and then kill with a sword.
Leevers are worm-like creatures that live in the ground, sticking their spiky heads up and trying to attack you. They hide underground, so be careful when you're walking around in an area that has Leevers, because they like to pop up right under you.
The Like Like is an ugly, bloated, huge, upright worm that will try to eat you. If it gets a hold of you, tap the A button to try to escape. Sometimes, the Like Like will steal your shield, or some rupees. If you can quickly defeat it, you might be able to retrieve your shield or rupees, but if you lose your shield, you'll just have to buy another one.
The Moldorm is a brown worm that moves around randomly and can be hard to follow or avoid.
Not to be confused with Moldorm, the Moldworm can only be seen when you're Minish-size. Moldworm is a worm made of pink segments, and it has an open mouth that will vacuum you up. Then it will burrow underground, hurting you while you're trapped in its wormy body. It will spit you out when it pops back up. Its head is its vulnerable spot.
These strange red and blue creatures look a little bit like dogs. They can only be seen at Minish size. They normally just wander around rooms, but if you come near, they will start dashing around haphazardly. The blue ones dash in circles, but the red ones try to approach you while dashing.
The good old Octorok has been around since the very first Legend of Zelda. There are blue and red ones in Minish Cap, and they walk around spitting stones at you as usual.
Another classic enemy, the Peahat uses a flower-like propellor to fly around the room, and is invulnerable to your sword while flying. However, the Gust Jar or boomerang can be used to defeat them. The red ones just fly around, but the blue ones carry items and try to drop them on you.
You only see these when you're Minish-sized. They look kind of like flies, and the float around until you come near, at which point they fly over to attack you. The blue ones carry blobs of mud and try to drop them on you, turning you black temporarily.
You can't hurt these mushroom-like enemies with your sword. They wander around, creating patches of sand from time to time. The Gust Jar can stun them and make them vulnerable.
The Rock ChuChu is a red ChuChu that has a big, spiky helmet made of rock. The helmet isn't very strong, though, because you can destroy it with just a swing of the sword, turning the Rock ChuChu into a regular red ChuChu.
Rollobites are like roly-poly bugs (also known as pill bugs) that will curl up into a ball if you hit them with your sword. You can carry them around while they're rolled up, but be careful not to hold them too long, because they do unroll eventually. You can throw a rolled-up Rollobite into a hole so that you can walk over the hole.
Ropes are snakes that slither around, and when one sees you, it will slither quickly toward you.
Sometimes you will see a rupee just sitting there on the floor. Be careful, because sometimes these turn out to be Rupee Likes, which have a fake rupee dangling from a tentacle-like appendage. Defeat these just as you would a Like Like. To check a rupee for fakeness, swing your sword at it. If it's real, you'll collect it, but if it's fake, it immediately turns into a Like Like. Swinging at a fake rupee with your sword gives you a chance to run away.
You only ever see one of these in the game: hovering over Gregal's bed. Nobody else can seem to see it but you and Gregal. The only way to defeat it is to pull it away with the Gust Jar. Doing so will make the Wraith disappear forever, allowing Gregal to recover from his illness and give you the Light Arrows. If you don't get rid of the wraith, Gregal will die.
Scissors Beetles are large bugs with blue manibles that they can throw at you like a boomerang. You can't hit them head on, because their mandibles block the attack. Once they shoot out their mandibles, run in and attack, careful to avoid the mandibles.
These simple, slug-like creatures slither around, leaving a trail of harmless slime. Sometimes they drop from the ceiling, so watch out for shadows.
The orange, glowing Spark floats along walls and can't be hurt with a sword. Use the boomerang, and the spark turns into a fairy.
Like the Bow Moblin, the Spear Moblin looks like a pig-faced human, but this type carries a spear. They can jab with the spear, or, if they see Link nearby, they might charge forward at Link with the spear raised. You can't hurt them from the front because they block the attack with the spear. Try to hit them from the side when they're charging.
The Spiked Beetle is invulnerable, but you can use your shield to make it turn upside-down, revealing its vulnerable underside.
Spiny Beetles can hide under bushes and rocks, and if you get near one (whether it's hidden or not), it will walk toward you. Be careful to look for suspicious bushes and rocks so you don't get hurt by one of these hidden creatures.
These grey ChuChus wander around like usual, but they have the ability to transform their bodies to stick out dangerously sharp spikes. They are difficult to defeat, because they become spiky when you try to attack. Your best bet is to stay close to one that is being spiky, and then strike the moment it retracts those spikes. Bombs also work well, even against their spiky forms.
These skeletons come in blue and red. They both jump around the room, jumping out of the way if you swing your sword, so they can be tricky to hit. The red ones throw bones at you, so be careful.
A red version of a Crow, this bird will attempt to knock into you to make you lose some rupees, and it will steal the rupee and try to fly away.
Tektites are spider-like insects that hang around on mountains. They jump around, trying to land on you.
Traps are mechanical, razor-sharp objects that can't be destroyed in any way. One type sits motionless until you come near, slicing across the path. The other type moves continually along a pre-determined track.
Wall Masters are red and look just like Floor Masters. However, they fall from the ceiling instead of wandering around the room, but they will take you to the entrance of the dungeon just like a Floor Master.
Wisps don't actually cause damage, but they stop you from using your sword if they latch onto you. The boomerang will make them vanish.
Wizzrobes, like in past Zelda games, will randomly appear and disappar in a room, showing up in random spots. They will aim a blast of energy (or fire or ice, in the case of fire or ice Wizzrobes) at Link. They can be defeated when they are visible, but just be careful not to be in the way of their blast. The ice Wizzrobes will freeze you.