Best - The Legend of Zelda: A Link to the Past
They returned to a top-down view, added a number of items and mechanics that would become series staples, and introduced the Light/Dark World concept. I don't really have to go into detail, but it's probably one of the greatest turnarounds in gaming history. I almost listed Super Metroid for similar reasons.
Worst - Final Fantasy XII
There are only two numbered Final Fantasy games that I can say I dislike, and this is one of 'em. From the MMO-esque ADB battle system to the character progression via License Board to the story and characters themselves, it's just not what I look for in a JRPG. Its few redeeming qualities were level and enemy design, and a pretty presentation in general (which is expected from a game so late in the PS2's life). I'd even consider XIII (which, for all of its faults, I enjoyed greatly) to be a step in the right direction.
If they can manage to replicate XII's exploration in XIII-2 like they say they are, then I think we'll be in for a treat. Not to mention Versus XIII on the way, which looks to be a great next step for the series.