From off the top of my head, I would say the 16th colossus, Malus, from Shadow of the Colossus. The music, atmosphere, and the sheer power of the firebolts were enough to scare the shit out of me. It was definitely different from other boss battles, primarily because it felt nearly hopeless to fight against such a beast.

Without a doubt I have never had so much fun fighting a boss until I came across the Goemon Impact Giant Robot Boss Battles of the N64 Goemon games. You start off terrorizing the countryside and doing as much damage to the landscape as possible to build up strength, then when your opponent robot comes in you wail on him with a hailfire of kicks, punches, nose bullets, (and if you manage to pull it off) a gigantic laserbeam that bursts from your chest and annihilates the opponent onto the other side of the screen as the sky turns black.

They can get very hard and somewhat intense as the games progress, but that right there is some good and seriously funny shit. XD

givin the dood some props...
 

I'm with Qwarky on Verdugo. He was definitely one of the most intense battles for me, simply because of the fact that I hate being chased... its amazing how I even got through that game... yet it's one of my all-time faves.

I'm probably the only one who would say this, but I still cant forget Bowser from the original Mario. that was just emotionally satisfying, given my age at the time.

Also, it may have been easy as hell, but the second boss in Starfox 64 (I think the big dood in space...can't remember his name.) was fun.

:guitarist:

Now...this is something that I really need to think about....

But I am going to go with the first Colossus in Shadow of the Colossus.

It was the first time that I played the game. Just had bought it, popped it into my PS2, spent some time figuring things out, and started to find the guy. So first, I am freaked out as I go into this HUGE valley, and it is all dark, so I am thinking, he is just going to be on the other side of this valley. And then it cutscenes to the first guy you face...and I am just sitting there, gaping...

That feeling of oh shit! was worth buying the game alone...

Deemor, or the final boss of Granstram Saga. You don't know him, or what he is until VERY late in the game. He just pops up as the last boss, explaing to you why things are the way they are. He talks a lot of shit and when the fight starts, he backs it up with phenominal power. He flies all over the screen(you're fighting in space btw) and the only way you can damage him is by using the sword charge attacks. Very challenging and fun all at the same time.

Not a favorite per se, but nonetheless interesting: among the boss units in Naval Ops: Warship Gunner (IGN profile) and its sequel, Warship Gunner 2 (official site (Japanese); TotalPlaystation profile), is a supercarrier named after and designed on the principles of Project Habakkuk. In both games, it exhibits regenerative capabilities akin to D&D trolls - that is, slowly regenerates any damage not inflicted by incendiary weapons; however, by the time I encountered it in both games, my battleships were capable of delivering sufficient damage-per-second to overwhelm this effect.

One of my favorites would have to be The Boss in MGS3. The setup was perfect, just perfect.

the two megaman Juno fights at the end of Megaman Legends. That was such a What the fuck moment that I've yet to have matched.

Juno didn't exactly seem like he'd have an ass reamer form but low and behold, there it was.

Ganon in Ocarina of Time.
The most epic, emotionally involving fight to be ever put on a videogame. EVER.

The Axem Rangers in Super Mario RPG.
It was not only an intense battle, I was giggling most of the time just watching them.

Ultimecia in FF VIII.
This was the very first FF game I played, so finally defeating Ultimecia at the end of disc 4 was extremely satisfying. The battle is long and hard if your levels are not very high. Quite memorable.

Any boss in RE4.
Seriously, all the bosses in this game are brilliant. And not only the bosses, the game is full of memorable scenes. The garden with the colmillos... the castle basement full of novistadors... the freakin' mine cart ride...
All awesome.

shadow of the collosus
every single boss battle in this game is nothing but an awsome memory. It's the second one that really got me into the game because it was first colossus that was so damn huge and being able to climb it and hear such heroic music got me pumped and made me believe that this guy can really do the impossible for his love.

Kingdom Hearts II
Roxas vs axel


Metal Gear Solid 3
snake vs boss


I'll think of more later

Okay, no way I can list every boss fight I really loved, but I'll name some games that had boss fights I really loved and pick a specific few that I particularly liked, of those.
May also include some miscellaneous bosses, too.

Metroid Prime - Flaaghra, Thaardus, Metroid Prime, and Meta Ridley. The latter was probably my favorite, just because my battle with him was so intense. I lived with only 7 life, no extra energy tanks.

Metroid Prime 2 - Giant bug (can't remember name; took me forever to figure out how to beat it), Quadraxis, final battle (especially with the final Dark Samus, I loved the way that ended)

Zelda: Link's Awakening - Boss of the Catfish's Maw (one of my favorites of all time), and the final boss Nightmare, which was just bad-ass

Zelda: Ocarina of Time - King Dodongo, Volvogia, Bongo Bongo, Twinrova (hilarious ending dialogue), and of course the epic finale

Zelda: Wind Waker - Helmaroc King, Gohdan, Molgera, and once again an epic finale. I've played that ending more than any other video game ending.

Mischief Makers - chock full of them, but Merco and Lupin deserve special note, and the surreal final boss.

Resident Evil 4 - the liquid nitrogen guy (too lazy to go back and check his name; I didn't kill him, but he creeped the shit out of me), the scorpion guy in the hanging thing, dude in the burning farm. Lots of good ones, really, though the final boss underwhelmed me.

Super Metroid - don't remember any of their names, but all of them were excellent

Metroid Fusion - Nightmare, I think is the name, and for being so weird and confusing and hard to beat

Kirby 64 - had some good ones, but I like the final boss most: awesome music, plus I had no idea what the hell it was. Is that an avocado coming out of its ass? They just put random shit together for that boss.

Kirby's Adventure in Dreamland - the nightmare at the end, both orb and vampire form. Loved that boss. Meta Knight also gets a mention, for this game and the others he was in.

Pikmin 2 - lots of fun ones: Giant Breadbug (cuz it cannot hurt you), Waterwraith (constantly terrifying), Titan Dweevil

Sonic (in general) - Dr. Robotnik. Cuz c'mon, he's basically every boss, and most of them are awesome.

Maybe drop some more in later, if I remember any. This is nowhere near all the bosses I like, but they're some of the most awesome-boss games out there.

Legend of Zelda: Link to the Past - Agahnim. This was the only boss whom you could not harm directly with your own weaponry. Pretty cool to say the least.

Legend of Zelda: Ocarina of Time - Ganon. Very amazing fight to the death. The music was awesome as was the setup for the fight and the fight itself.

Metroid Prime - Metriod Prime. This required changing to the right weapon while dodging its attacks, plus the cutscenes in between were pretty cool, because while Prime tried to escape, Samus kept jumping down after it.

Kingdom Hearts - Sephiroth. I spent so damn long leveling up to beat this guy it wasn't funny. Eventually, I had to look up a strategy online and that still wasn't a guarantee to beating him.

Kingdom Hearts II - Organization XIII. Any fight that involves you fighting a member of the Organization (like Axel) was memorable. At least once a week I go back and try to fight them (I have a save file before any fight with an Organization member). I still have trouble defeating them, especially a certain black haired one who uses spears.

Chrono Trigger - Lavos (final battle). Quite possibly the best turn-based RPG fight I've ever played. The background was freaking amazing, the music was awesome, and the boss was tricky. I keep finding new ways to defeat this guy. :P

Metal Gear Solid: The Twin Snakes - Psycho Mantis. Even The Boss from MGS3 can't top this fight. He read your memory card, made your controller vibrate, started making people in pictures laugh. "Blackout" was freaking crazy, he used various objects in the room to attack you with. All the while, he could read your every move so guns are almost nullified. There's a trick to beating him, but I'm not gonna spoil it. I HAVE beaten this boss without using the trick, but it took me around 40 minutes. Truly one of the most amazing and innovative boss fights ever.


I'll list some more later, especially some Sonic ones.

Kintaro from MK2. Ridiculously cheap, but always very rewarding when defeated.

My favorite is the fight with Romeo Guildenstern's second form. One, because it's damn hard, and two:

Both of the Paper Mario games and the Mario and Luigi games have some pretty kick-ass bosses. Hooktail, General Shy Guy, Lava Pirahna Plant, a soda beast, and my personal favorite, a stomach.

i'd forgotten about the General Guy battle in Paper Mario. Everything about that is hilarious from the introduction (hordes of Shyguys doing baby screams), to the concept (you're battling a giant electrified baby buggy for cripes sake), to the shyguys actions (Shyguys on Stilts! :D), right down to the dialogue (YOU SIR, ARE RUDE!)

Next to anything that has to deal with Fawful from Superstar Saga (who is awesome simply by default) that has to be one of the funniest Mario boss battles ever.

Also making the memorable-duel list: the very last ace you confront in Ace Combat Zero - quite aside from the very cool music, strict time limit, and the fact that this is the only ace with more than one special weapon (three, in fact, one used exclusively for each phase of the fight; two of them can ruin your whole day)... well, there's something to be said for a dogfight where jousting is pretty much the only viable tactic for two out of its three phases (the special 'weapon' used in the final phase makes all attacks - including, oddly enough, cannon fire - from any angle other than head-on ineffective).

I'd say my favorite boss fight is either M. Bison from SF2 or Sephiroth's LAST form in FF7 (the one where you get to omnislash him and he just dies). Since you really can't call that last scene in FF7 much of a fight, I guess that leaves me with M. Bison from Street Fighter 2: The World Warrior.

I remember sinking quarters into the SF2 machine at the local arcade and being cheated in more ways than I can count by Bison. He is the kind of villian you just loved to hate back in the days before anyone had ever heard of "Champion Edition" or "Akuma". He would nail you to the side of the screen with a stream of double-kneepresses, cheese your life away with the Psycho Crusher when you blocked, and throw you out of just about anything. SF2 joysticks were broken all across the world because of Bison's cheap tactics; no one can dispute that.

Thankfully, he was made easier in Champion Edition and future versions of SF, but remained a cheap @%^* when controlled by the game's AI.

My favourite boss battles are as following:

Star Ocean Till The End Of Time - Norton because this is the first boss your fight and Cliff comes to help you making it so easy

Lion King - Scar because you get to throw him into the fire plus you seriously cant die from so many hits in the game

Lol no i havent cause i only recently bought the game 1 week ago yea i found it which was kinda rare for me and so of course i wouldnt play it on universe or 4th dimension and i dont really care about battle trophies

I can barely remember any of the old games with their boss fights since I haven't played them in a long time. I know fighting Sephiroth in FF7 was an enjoyable one though.

Fighting Kefka in FF6 was cool too. Jon Irenicus from Baldur's Gate II was also interesting.

Agreed on Irenicus, but I found Sarevok and his gang from BG1 to be far more challenging and interesting. Irenicus was just not as good of a villain in terms of challenge. Once you got his cheesy spell shields down, he was toast.

I've read through all these posts as I had difficulty deciding whether or not I had any 'fun' boss fights. Now that I think of it, Kingdom Hearts II is the only game I've ever played where the boss fights are enjoyable. I especially liked battling Sephiroth at level 79 countless times before finally taking him down.

On the subject of awesome boss fights, while I haven't played this myself, I'm sure you'll all aggree that this fight ranks high up after you watch it.

http://www.youtube.com/watch?v=7Yz_Oi_6w0Q

Now if only Nintendo would release a similar final boss.