Part 2 died, so here's Part 3!
You give clues as to what this boss is, and if someone answers correctly, they provide new clues, etc.
Here are your first clues:
I borrowed Amy's hammer for this battle.
Shafts of wood can help or hurt.
You can't reach me from the ground.
Wow, I got one, I think. Is it Sonic 2's Aquatic Ruin boss?
-Jake
Yep! ^_^
Your turn!
My clues:
"I keep something valuable in my chest."
"Beware, lest I sneeze on you!"
"Ouch! You spun into my knuckles!"
Hope these are good clues.
-Jake
Sonic Advance 2, Sky Canyon?
The Death Egg Zone Finale.
1) The Master Emerald
2) FLAMIN SNOT
3) Spin Dash into his hands is faster than jumping.
*kicks the game topics* There's no way in hell you're no right, John. Just continue.
Yeah, John got it. You're up, dude.
-Jake
Oh goody goody gum drops
1) Chase Me!
2) Underwater
3) Metropolis Precurser?
Tidal Tempest boss!
1)You first chase Eggman in his eggmobile through a maze
2)You follow him down into the water
3)He has bubbles around him like the spheres of the Metropolis boss.
That was quick 
Go! Go! Go! Go!
Next poster gets my go. =D
Voila.
ETA:
1). Precedent
2). Harrison Ford
3). You'll see it again and again
The Ball swinger from Green Hill Zone, Sonic 1?
Curses, I make this too easy. Yeah, it's your go.
WTF Those clues made no sence at all. Can I have an explanation?
1: Precedent means an example. It sets an example for the other bosses!
2: Harrison Ford. In Indiana Jones, Harrison Ford ran away from a huge boulder. Originally, Robotnik's ball weapon was going to be a regular obstacle!
3: You see it two other times, in Sonic and Knuckles and Sonic Advance.
Sonia, are you and Matt conjoined at the brain or is there just one of you and you have an account for both of your personalities? That was amazing...
Anyway, Sonia, I believe it's your go.
-Jake
No, I just know this stuff 
I can't think of a boss right now
Heh, yep, Sonia got it in a nutshell. Anyway, Sonia or eavy and Bomb can go, whoever feels like it first.
1- Oh crap!
2- This boss bugs me... <<
3- Limp Bizkit style in da' house yo'!
Meh. I think it's too easy.... <<
Sonic Rush, Eggman/Eggman Nega. In Mirage Road. It's a dung beetle! Ew!
Bingo. I knew that was too easy.
Your go Were.
Ok, here goes. I think this one might be easy, too.
1) This isn't a playground, you know!
2) Jeez, Knuckles could use that thing better then you!
3) One shoots, one doesn't. The other kills. No question.
Knuckles boss, Sky Canyon, Sadv2
Yeah...you're go.
1) If I get dirty, you'll miss me
2) Back defense
3) ZARP
Oil Ocean boss from Sonic 2?
It might be, can you explain why you think it's Oil Ocean?
Well...
1. When ol Dr.R dives down in to the oil quite naturally he gets dirty and and you cant hit him so you'll miss him.
2. After he dives that claw thing comes out from behind you(I think)
3. Then you have the laser the gun that tries to 'ZARP' you 3 times in a row.
Well thats what Im thinking anyway.
not really, but eh, your go anyway =p
Ill give up my turn since I cant really come up with anything...however I am curious to what the real answer is Matt.
Well.
1). You can jump down into the oil and hide under the ledge by continually jumping. It's easy to avoid Robotnik's laser this way.
2). He has a spike on the back of his submarine craft.
3). This one was right =p
Anyhoo, here's another:
1). Destroying it only makes it harder.
2). Two is better than one.
3). Don't stand still for long...
I'm guessing it's the Launch Base final boss in Sonic 3, without Sonic and Knuckles locked on.
1). Destroying it only makes it harder.
When you destroyed the laser shooting part, Eggy comes back with the second part.
2). Two is better than one.
Two parts to the battle?
3). Don't stand still for long...
If you stand in one place, you'll either get scooped up in the hands or you'll get hit by spikes when he's strafing the bottom of the screen.
The boss from Flying Battery zone, act 2?
1) Destroying forces you to go through a mini obstacle where you must make it to the top without getting smashed. And the second part of the battle is a little harder.
2) It has two parts to the battle.
3) The first part of the battle requires you to dodge the laser by stopping. But if you wait too long, it'll blast you. This may also refer to the second part of the battle, where Eggman's mech has spikes that moves across the stage, and you have to jump them.
Nope and nope.
Lava reef zone act 3? I'm just guessing now.
Nope.
Here's another:
4). Quick, save me!
The race with Metal Sonic from Sonic CD?
You wouldn't stand still for too long because otherise you loose. Quick, save me would refer to Amy. The other clues don't make sense though... <<
Final Fury for Metallic Madness in Sonic See Dee?
1) The Legs of the Main boss gets more and more aggressive
2) 2 Legs are better than one for hitting Sonic
3) The Beginning of the boss has the Firefly badniks trying to hit you.
4) Amy appears at the end.
Nope. Here's another clue.
5). In other circumstances, it can rise up and down.
Perfect Chaos! It all makes sense! (if it doesn't, I have a couple more guesses)
1) The second part of the battle is harder. Also, each hit blows it up, and then it comes back, hitting harder then before.
2) It has TWO tentacle things.
3) You wait too long, you run out of rings.
4) I have no idea.
5) It can rise and fall in the water stuff.
No.
6). You'll be here again
Bigs battle with Chaos 6?
1). Destroying it only makes it harder.
Parts of the arena get destroyed, which you see when Knuckles fights Chaos 6.
2). Two is better than one.
Not sure...
3). Don't stand still for long...
I think this is a basic for any boss battle.
4). Quick, save me!
Save Froggy!
5). In other circumstances, it can rise up and down.
The Egg Carrier?
6). You'll be here again
You fight Chaos 6 with (Chronological order) Big, Sonic and Knuckles.
Nopers.
I wanna say Knuckles' Master Badnik battle at the end of Launch Base act 1. To lazy yo give reasons. I will if I'm right. 😛
Nope again.
7). Mega Drive
Silver Sonic in Death Egg Sonic 2?
1). Destroying it only makes it harder.
Because after it comes the big Egg-suit thingy, which is harder to kill?
2). Two is better than one.
Two consecutive bosses.
3). Don't stand still for long...
Well, yeah, applies for all boss battles
4). Quick, save me!
After you defeat both bosses Sonic falls through the atmosphere and Tails comes to rescue him.
5). In other circumstances, it can rise up and down.
No idea. o.o
6). You'll be here again
In Sonic 3 and Knuckles.
7). Mega Drive
Self-explanatory.
Is it Mecha Sonic in Sonic 3 and Knuckles
1) Sonic and Knuckles destroyed it once but then it turned super with the power of the Master Emerald
2) Sonic destroyed one Knuckles destroyed another
3) Theres a bit when if you time it right Knuckles looks like he is moving but he doesn't move
4) Angel Island is falling
5) Sonic's Sky Sanctuary is very unstable
6) Sonic fights him, Knuckles fights him
7) Mega Drive. And PC as well.
Nope!
8). Stop - Sonic Time!
