Bosses of The Legend of Zelda: The Minish Cap
The bosses of The Minish Cap are "different", to say the least. Each battle is very unique and original, even for a Zelda game. In fact, you end up riding inside more than half of these bosses at one time or another during the battle! To make things easier and less confusing, here is a list of the bosses, and the best possible way to defeat them:
 Big Green ChuChu
The boss of the Deepwood Shrine is actually just a regular ChuChu, but due to your miniature size, a simple enemy has become a long and difficult boss battle. In the first stage of the battle, the boss will simply waddle around the room. Use your Gust Jar to suck up the jelly at the boss's base. Once enough of the jelly has been sucked out, the ChuChu will become top heavy and begin to stagger back and forth around the arena before falling on its side. Be very careful during this phase, as it tries to land on you, and considering its size, it's pretty hard to avoid. Anyway, once it is down, start slashing at it with your sword as fast as possible. After the boss gets back up, repeat the process as many times as needed. Later on in the battle, however, the ChuChu will begin jumping up in the air repeatedly in an attempt to squash you. DO NOT try and suck up the jelly at this part, as it leaves you extremely vulnerable. Instead, wait for it to stop jumping, and it will go back to just "waddling" around the room, making it open to more attacks.
The boss of the Fire Cavern is easy once you figure out how to damage him. First, make sure you have your sword and the Cane of Pacci equipped. Next, when the boss prepares to attack you (by firing lava from its mouth out at you), run around the room to a point where the boss's side or back is right ahead of you. Fire the Cane of Pacci at the boss's shell, and it'll flip up on the air and land on the boss, stunning it. Use the boss's head/neck as a bridge, and run up and slash him repeatedly. When he starts to shake, run back to solid ground, as it means he is getting ready to regain consciousness. As the battle goes on, the boss will use a few new tactics as well, such as making the lava pool flood the arena, or using a more powerful flame breath attack. Just be prepared for these new attacks and continue with the same attack method and you'll eventually win.
Mazaal is the boss of the Fortress of the Winds, and is actually quite easy. To defeat him, you must first take out his two hands, which move across the arena using various attacks trying to crush you. Use your Bow to fire an arrow into a hand's "eye", and the hand will become temporarily disabled. Run up and slash the "eye" repeatedly until it is dismantled. Do the same to the other hand, and Mazaal will become disabled. Use one of the two Minish Portals in the arena to shrink yourself down, then run into the boss's head through the mouth. Inside, you will find six columns and (possibly), dirt. Use your Mole Mitts to clear away the dirt if necessary, and use your sword to attack the column that is glowing at its base. Eventually, the column will explode, and you will be spit out. Repeat this process three times to be victorious. Like the other bosses, Mazaal has a few new moves which he uses later on in the battle, such as a sweeping breath attack which automatically turns you to Minish size. Just be careful and carry out the same attack plan.
 Big Octorok
As soon as you free the Water Element, the Big Octorok near it will thaw as well and suck up the Element, retreating into the next room. Follow after him to start the next boss battle. At first, the Octorok will just fire large rocks at you, similar to the Octoroks in Ocarina of Time. Use your shield to reflect them back at it. Once you have hit the boss three times, he will become partially frozen and move slower (although he will still attack). Run behind him, and light the long flower tail he has on fire with your Flame Lantern. The boss will bounce about the room a few times, before refreezing. Repeat this process two more times (firing a total of nine rocks back at the boss) to defeat him. Just watch out for his new moves, though. He starts sucking you in and spitting you out, and it's unbelievably hard to predict whether he is going to use the Suck attack or shoot a rock at you until the absolute last second, so just be careful. He also has an ink attack which he uses to make the room dark, but just light your Flame Lantern to solve that problem.
This entire battle takes place in the air, and you are, ironically, forced to rely on riding on your enemies' backs in order to avoid a long drop back to the Palace of Winds below. Anyway, make sure to have your Sword and your Roc's Cape equipped. This battle is fun, frantic, and fast paced, so just try as hard as you can to keep up with your enemies, as you can literally die within a minute if you aren't careful and you don't watch your step. You have to take turns riding/attacking each boss, and the means of damaging each of them are very different. To damage the large (red) Gyorg, you must "match" the eyes he has open. He will open three eyes at a time, and you must use the Split Platforms on him to separate yourself accordingly, so you are able to attack all three eyes at once. Once all of the eyes have been damaged, all of the Gyorg's eyes will open. Continue slashing the eyes with your sword until the boss begins to explode, and the blue Gyorg appears to pick you up. Watch out for the blue Gyorg's sweeping attacks as you attempt to damage the red Gyorg, as well as the small, green Gyorgs that fly back and forth as well. To damage the small (blue) Gyorg, attack whichever of the four eyes opens with your sword. Keep an eye out for its tail, as it can both damage you and knock you off. Whenever it begins to swing its tail, use the Roc's Cape to jump (JUMP, not FLY, as flying can make you go too far and end up falling). Just continue attacking the eyes and dodging the tail until it takes you back to the large Gyorg. Just continue these patterns until both bosses are defeated. If you fall off, it's not really a big deal, as you just lose a bit of health and reappear on top of whatever Gyorg you were just on. Still, a lot of falls can really add up, so be careful.
Vaati's first form is, in my opinion, the hardest. He has a plethora of attacks, such as a sweeping fireball attack and a laser beam strafe. The best advice I can give you in this battle early on is to not rush into it, and to take your time getting a feel for his different attacks. The eyes that rotate around him only stop moving when they are preparing to do the laser beam attack, which can be extremely deadly if you are right infront of them at the time (thankfully, they only fire straight ahead). Anyway, to damage Vaati, you must first destroy the small eyeballs that rotate around him on the floor. Any sword attack will do, but I urge caution and precision while doing so. Once the eyes are gone, Vaati's weak point will appear (a large red eye in his... stomach?). Repeatedly attack it until it closes, and the small eyes reappear. Repeat the process until Vaati transforms, but beware, as his attacks become more vicious and unpredicatable as the battle goes on.
 Vaati Transfigured
This is a welcome break compared to the last battle. Vaati has changed his form, and the arena, the main feature to the new battlefield being the flashing Split panels in the center. You're going to have to use them to damage him, but first, you have to reveal his weak point. Fire arrows into the eight eyes surrounding him, and they will either turn red and open, or turn blue and stay shut. If they turn red, they're vulnerable for sword attacks. If they turn blue, they're staying shut, at least for now. Four of the eyes will turn red, in some sort of shape which you must match with your three dopplegangers (similar to the method used against the Red Gyorg). Use sword attacks with Four Links against the eyes all at once to make the main eye vulnerable, then repeatedly attack it with your sword until the eight outer eyes respawn and you must repeat the process. Vaati's attacks at this point include a shock attack which moves slow and can be avoided easily, an "avalanche" attack that makes rocks fall down from the ceiling, and an attack where he fires large dark 'rocks' at you. Wait until these dark rocks land on the ground, then use your sword to break them apart, as they often contain helpful hearts or arrows. Anyway, after defeating Vaati in this stage, you earn your first breather since you opened up the Boss Door. Enjoy it, as the worst is over, but the final final battle is right around the corner...
 Vaati's Wrath
Vaati returns, blocking your escape to the Elemental Sanctuary, and transporting Link to a new battlefield. The two Minish portals and the four Split panels should be obvious and expected by now. Vaati's attacks are of similar nature as the ones he's used before, except his new arms pose a threat. So the arms will be the first to go. When Vaati burrows his arm into the ground, avoid it when it comes back up and use the Cane of Pacci to flip it and seperate it from Vaati. Then, use the Minish portal to shrink down and run into the all-too-convenient doorway in the arm. Once inside (you may need to use a Flame Latern to see), there are many Vaati Spawns frantically running around the area. They are all indestructible, aside from the one with the glowing red eye, which can be picked off with a sword attack or two. Once it is destroyed, the other Spawns will die as well, and the arm will explode. Destroy the other arm in the same fashion, and then focus on Vaati's body. He's now limited to two attacks: a sweeping lightning ball attack, and an attack where the four smaller eyes shoot energy balls simultaneously. Sounds like a job for Four Links. Use the Split Panels to summon your dopplegangers, then wait for the four eyes to shoot the energy balls out. Line yourself up with them, and swing your sword(s) to deflect them back at Vaati, stunning him. Run up and use your sword attacks repeatedly until he's defeated. Congratulations, you've beaten The Minish Cap!