I haven't played Runaway 3 yet, but I heard it doesn't continue the ending of 2. So there's another one...
And Dreamfall, and KOTOR2.
Basically all games whose ending where made for sequels, yet the sequels never came...
Sam: "We're 98% certain General Skun-ka'pe is evil."
Stinky: "And the other 2%?"
Max: "That he's crazy and we have to shoot him! But that may be wishful thinking on our part."
(Any resemblance to KOTOR is purely coincidential, really!)