Best JJ1 level: the Dreempipes ones. I have always liked those for some reason.
Worst JJ1 level: Scraparap. I hate, hate, hate, hate those tiny flying things that shoot RFs at you and follow you throughout the entire level.

And I am glad to see that I'm not the only one having trouble with that one jump in Orbitus 2. It is the only part in the entire game where I need a cheat code (heck, even the Episode 6 boss is easier).

Best JJ2 level: I never liked the JJ2 single player very much, but I suppose I can live with the Beach levels.
Worst JJ2 level: death to the second inferno level (the one that comes after a cold day in heck)