for the below, with green be the output and red the input,
green peaks at 654.248m, dips at 461.173m
red peaks at 550m, dips at 450m

would you say the gain is ~2?

 

Yes, you would.
This is the definition of gain on most transistor amplifier circuits.

 

Original question: AC input at zero bias + - 1 V , AC output 3V bias + - 1V, gain
= 1?

Yes, you would.
This is the definition of gain on most transistor amplifier circuits.

Sorry for changing the original question.

But what if the peak of the output curve saturates at a certain value say
you have AC input at zero bias + - 1 V, but output voltage that is in the range of [3.5 : 2], so it is no longer [4 , 2], would you say the gain is (3.5-2) / (1 - -1) = 0.75

 

No, you measure the AC gain while the input is still undistorted. It is the job of the amplifier designer to ensure that the circuit with gain A won't saturate with in input with amplitude Vin. In fact, the maximum input amplitude that won't be distorted is a specification for each amplifier.

 

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