JJ1 Best: That bonus level where you get 10 seconds to collect 45 gems. Among others. Really, most of the bonus levels were cool. If only they had working difficulty settings.
JJ1 Worst: Orbitus 2. I have never once completed that level without the airboard code. Never.

JJ2 Best: Can I just choose all of Episode 2?
JJ2 Worst: Uhhh... the unfinished Psych secret level.