If Not

[FoxEye]

The first one.

Also, pretty sure the original sentence should read "one of, if not, my favourite games of all time"

I'm pretty sure it shouldn't read that at all

"One of my favourite games, if not my favourite, of all time."

Much better

As to the 2nd meaning, I can see how that might come about.

"If not my favourite thing ever, I do still like it." (would mean the same as...)
"It might not be my favourite thing ever, but I do still like it."

Guess it depends on the context (as usual).

 

[Smigly]

I pick option A.

 

[Duff-Man]

As others have said, the first interpretation.

The second would be: "...one of my favourite games, though not my favourite"

 

[arctine]

Isn't favourite an absolute state? You can favour several but only one can be your favourite?

 

[dfarrall]

The first of course.

 

[Cosimo]

The first is favourite of all time.