This is a tough one. I like many properties that have been licensed for various systems that I’m not a huge fan of.
For example, I like Firefly, but Cortex Plus is only so-so, in my opinion.
I like Dresden Files, but not enough to play it.
I like Wonder Woman, but DC Heroes isn’t the best system.
I wouldn’t have found Atomic Rob, War of Ashes, or Mouseguard if not for their RPGs, but I’m not super into them as properties (yet).
Call of Cthulhu is a game that gets its own licensing– if a game company licenses the property that is another game, does that count as a favorite licensed RPG?
If so, then my current favorite is either Cthulhu Live or Trail of Cthulhu.