I'm looking for some more games that really go in depth of single player boss battles. I want something challenging but at the same time I want each fight to be unique and take a lot of skill to defeat each boss ( or at least make it a fun experience / feel rewarding ). Some games that come to mind are Zelda, Dark Souls / Demon Souls, diablo. I just want to create an epic mmorpg style boss battle but tone it down into a single player game. Right now for my game I've mostly been creating encounters that deal with avoiding lots of objects. Other ideas I have are destroying objects before extra monsters spawn, curing debuffs in specific areas, ect. So I guess if anyone else has other games they know of that focus on single player boss encounters please chime in. I've been focusing on all the core mechanics of my game and now I just need to layout the rest of the boss fights on paper before I can finish coding the rest of them.
Single player boss battles?
That's the entire premise of "Shadows of the Colossus". There are no regular enemies - just 15 or so boss battles, each one mostly unique from the others.
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The battles last a long time, so jump to 2:30 to get a better idea of the feel of the game.
Also, Sonic Adventure comes to mind, but to a much lesser extent.
(One boss) http://www.youtube.com/watch?feature=player_detailpage&v=lf2lreqZxhc#t=379s
(same video a few minutes later, another boss) http://www.youtube.com/watch?feature=player_detailpage&v=lf2lreqZxhc#t=424s
...I was trying to find a certain boss in particular, where you have to chain-attack along the flying snake's spin, but I can't find it.
I'm sure there's probably some interesting boss mechanics in Mario 64, I just can't think of any.
I guess you can watch through this and see:
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If you're not restricting yourself to 3D examples, you can take a look at these
-Megaman series
-Alien Soldier, Contra: Hard Corps, Gunstar Heroes( the "seven force" in both gunstar and alien is badass )
-Castlevania series
2D games (especially older ones) seem to have the coolest boss-fights.
the Zelda-series, it's got a fair amount of bosses, but a lot of the "regular" opponents are unique/individual as well.
Zelda
Megaman X series
Metroid
Castlevania
Breath of Fire series
Star Ocean Til the End of Time
Crono Trigger
How about....every game ever.
You seem to be confused thinking that boss battles are an MMO thing.
Pretty much every boss fight seem to follow the same pattern:
1. Figure out the boss' attack pattern, and counter it. (attack patterns might include minions)
2. Find the weak spot(s) and exploit it.
3. When boss gets low on health, it gains extra epic attack patterns.
Then its mostly a question of making the boss fit with the setting of the game, and make it appropriately epic for how far you have progressed in the game.
Often you get to show off your skill with newly acquired equipment.
Lots of room for variation on all three points, only imagination sets the limit.
How the fight is done will depend a lot on the core game mechanics in the game, you want to let the player show off their skill using them.
The level is practice, the boss is the exam 
For another game that focuses on bosses (though 2D too), there's Alien Soldier:
Gameplay starts at 5:23. Yeah, the first levels have some enemies in it (mainly to stockpile some ammo and such), but eventually it reaches a point where it's purely bosses.
