Worst: Sorry, no contest on this one ME3. Massive universe full of hinted at possibilities for the ending, and they go with something completely out of left field, then give us an A, B, C choice factoring in nothing that we've done. Even with my high hopes for the DLC "expanding" the ending, I still seethe to think on the ending.
After that probably Skyward Sword, though I'm a little biased there. Whatever land you want to call the setting of SS, it wasn't Hyrule and fails to so much as hint at how things change.
Best: Portal 2. The perfect ending for the game. It suited everything in the damn game so damn perfectly.