Back in my day, bosses were barely bigger than Link, and the only way you could tell they were special was that that made a funny noise! I also had to walk uphill both ways to my dungeons, above my head in snow - but, it looked more like large squares than snow flakes - etc, etc.
Nowadays, kids want their fancy-pants "big enemies" with "music" and whatnot. Bah, fine.
Ok, ok, I'm not really that old. In fact, I like my bosses to be set apart from ordinary enemies too. This includes giving them boss music, fancy death effects, and the like. In this three part tutorial, I'll show you the ways to set your bosses apart.
Keep in mind that the term "boss" is subjective. A Darknut or three placed strategically in the second level can be just as much a boss as a Dodongo. It's all up to you. So, without further adieu, on with the show!
A boss is a special enemy or group of enemies that the player must defeat to progress in the game (usually). Generally, they're stronger than their brethren in the level, and guard precious treasures that are either rare (Heart Containers, etc) or otherwise impossible to acquire (weapons, etc). The key thing to a boss is that it have a reward. Be it an item, passage, or bragging rights, the player has to have a reason to keep dying over and over to beat it (or not, if they've been through the game before)
So, why not put a boss guarding your dungeon item? Which makes a better impression on the player: having the hookshot lying on the floor, where any old hero might pick it up, or guarding it with an Aquamentis (with fire statues and traps!), whose death causes a treasure chest to appear with the hookshot? I think you know what I'm getting at. (I'll talk about how to do this later)
Another key thing is that your boss must be different from the other enemies. As I mentioned before, a couple of Darknuts early on might be a boss, but in Level 7 where the player's already faced scores of Darknuts, and worse, they don't hold quite the clout they might have earlier.

Now, a Death Knight (the Level 3 Darknut, new to Zelda Classic) might up the ante a bit, since it moves considerably faster and has more HP than even a Blue Darknut.
And, of course, there's music. You know something's up when the music changes. Heck, in the original Zelda, just stepping into Level 9, with its special music, told you that you were facing a great challenge. So, pick a tune to be reserved for bosses, and play it for the boss room. (Again, I'll talk more about this in a minute)
So, in summary, a boss is an enemy, or even a puzzle, that meets these criteria: