Over the last decade or so, I've played a lot of games. The following are the bosses that I consider to be the most ridiculous and most annoying to fight. Simply either because they are ridiculously tough or just have an annoying ability that is difficult to counter. These bosses tend to be extremely cheap or overpowered or both. Final Fantasy didn't make it to the list because of Auto-Life and Armaggeddon spam. You know what I'm talking about if you've ever fought that boss.

1) Shin Megami Tensei Series (Digital Devil Saga, Nocturne, and Persona dunno about Raidou)

Boss: Almost any fight but especially the cameo battles

These bosses are loaded with the cheapest and most powerful attacks with almost no way to counter them except through trial and error. In the special optional boss battles, the boss will consider any abilities that nullify or absorb an attack to be a cheap shot. In response they will instantly kill your entire party (9999 damage to everyone when max hp is 999) until you restructure your team. Most of these battles are a test of endurance against an enemy with insane damage. You have to be careful because if the battle drags out too long, they will use the instant kill attack anyways.

2) Atelier Iris

Boss: The 3 Golden Pigs

The 3 Golden Pigs might not look tough, but they each pack the power of an end game boss and the most insane speed in the game. If you can take a beating, it isn't a test of endurance but their power is so insane, even the last boss is easier to deal with. Not only are they fast, but they have a high probability of activating the "quick" ability which halves the time required for their next turn. On top of that, they have a high chance to stun your characters. Combined, they are extremely deadly although they don't have many special abilities. Unless your characters are equipped with some of the best customized items in the game that you have to spend hours to create, you probably won't beat them. Still, this is one of the few boss battles that rely on preparation and skill rather than luck.

3) MS Saga: A New Dawn

Boss: All late game bosses

The game itself wasn't that great, but the bosses were ridiculous end game. No matter how tough it looks, it will kick your ass. Everything just had the absurd power to wipe out 1/3 or more HP of all your characters in a single attack. One of the characters mentions "It's a Zaku" (the weakest type of unit in existance). The problem is that this one is black and piloted by one of the most badass people in the game and the characters go what the hell as well. It didn't matter how tough they looked or what you were in, they were just overpowered. It also doesn't help that the max level is 50 and the final boss was still insanely strong with his ultimate attack. If you don't have the alternate universe mobile suits (the strongest in the game), you won't get far. The special bosses in this game include Burning Gundam (melee attacks nearly 1HKO anything) and the bosses of the optional dungeon.

4) .hack//G.U.

Boss: Doppelganger

The Doppelganger is an optional boss that appears if you don't move for a long time. It's a clone of the main character Haseo but is always several levels higher, uses the same weapon as you, and has insane HP regeneration. If you prepare a set of decent equipment and an Awakening before hand, he's not tough. That is unless you decide to use a weapon besides your Dual Daggers then you're basically screwed. However, each time you beat him, you get a powerful item. If you beat him in all 3 games, you get rewarded with the armor and accessory that basically makes you unstoppable like the Doppelganger. The reward is well worth it if you can handle it.

5) Shining Force EXA

Boss: The Final Boss

I'm not going to reveal his name to avoid spoilers, but its just the final boss. He's not that tough except the cheap shot attack. If it weren't for the cheap shot attack, he wouldn't be really tough. In his cheap shot attack, he turns into dark aura and just homes in on you. Each attack hits for 15000+ damage if you do not have a very strong resistance to it. If you're playing as the melee character, you are guaranteed to get hit at least once. Twice if you're using a slow weapon. If you're using the range character, its easier to avoid presuming you don't accidentally run into the wall. Of course you can always just use a Light Charm (temporary invincibility) when the boss uses that attack.

6) Valkyrie Profile: Silmera and Star Ocean 3

Boss: Freya

Although Freya is optional in both games, Freya is by far the toughest of the bunch. Freya appears as the ultimate secret boss in Star Ocean 3 after defeating the Ethereal Queen and appears in the Seraphic Gate before the Ethereal Queen in Valkyrie Profile. They both have the same abilities in common though. That ability being some of the most insane area spamming skills you have ever seen featuring massive damage and stun rates to boot. On top of that she has one of the largest life bars in the game to back it up. Even with some of the best equipment, it is impossible to win without figuring out the strategy to beat her in either game.

7) Nippon Ichi Games (Disgaea, La Pucelle, Makai Kingdom, etc.)

Boss: Baal the Uber Prinny (or Pringer X same thing really)

Baal is probably the incarnation of cheapness. Ridiculous stats, ridiculous HP, and for the most part, the first turn basically decides whether you will win or lose. He tends to appear as level 4000 after you beat his normal form but he is so strong that he can probably beat your level 7000 team that has been reincarnated several times. The culmulation of his cheapness appeared in Disgaea 2 where he appears with 4 standard Baals in addition to the Uber Prinny. His skills tends to hit for over a million damage and most characters won't even have that much HP even if they had the best multipliers. Thankfully he is optional but all the best stuff tends to require you to go through him at some point though.

8) The Last Remnant

Boss: The Enlightened Seven

This game is the reason why special bosses should only come 1 at a time. The Enlightened Seven are 7 bosses you have fought before powered up several times over and equipped with some of the cheapest abilities in existence. The most common ability being instant killing groups. Each of your 5 man teams will probably be down each turn and it doesn't help that they have ridiculous damage as it is. Not to mention the final 2 spamming team attacks frequently. Of course, many of these abilities can be avoided by using your own cheap shot to counter it so they can't use it on their turn. The good part is that once you beat them, you can recruit them for your team and use the abilities for yourself. The problem is that its so late in the game that you probably can't even upgrade them to the fullest of their abilities.

9) Wild Arms 3

Boss: Ragu O Ragla

Nothing is annoying as having to fight the same boss twice in a row. The second time he is powered up several times over making it even worse. Of course, it also doesn't help that he is at the bottom of a 100 floor with no save points and only the option to return to the surface at specific floors. The only reason he is annoying is because of his absurd damage. If you don't have the items to neutralize damage from his attacks, you're dead. Period. No questions asked. 1 hit will deal over the max possible HP you can have and odds are you might only have 1/2 of that as your max. Either way, you're probably still dead. The first form just sticks to fire element so its easier to counter. Unfortunately the 2nd form is fought almost immediately after and uses all elements now.

10) Kingdom Hearts

Boss: Any on Hard Mode

There is a huge difference in Kingdom Hearts between normal and hard mode. All the bosses might as well be equipped with a 1 hit kill skill. Keep in mind this is the first Kingdom Hearts so you don't have reaction commands or insane special abilities to help you. Even normal enemies don't hit anywhere near as much. In hard mode, the bosses feel like the developers got lazy and just gave everything 1 hit kills while weakening Sora''s overall combat abilities. Just try to dodge and hope you don't get hit so you can beat them.