ALL of the plots are good but There's a tie between Amy+Kif and Fry+Leela
I like the Leela's parents thing because without it there wouldn't be any "Leela's Homeworld", which made me cry almost.
"Where The Buggalo Roam" and "Amazon Woman In The Mood" have to be the best examples of Kif and Amy (Haven't seen "Kif Gets Knocked Up A Notch", I started watching FOX since "Less Than Hero", weekly, anyway)
The Why Of Fry had Fry and Leela's "First REAL Kiss" and 4ACV14 (I think, or was it 18?), the series finale, will be the CAP of it. Fry's future thing AND the Nibblonians (SEE "THE WHY OF FRY" ) are both good plots too.
Nixon has been a, what I call "Unmain character" meaning he's in at least 6 episodes or less. Amy's parents are good "Unmain Characters".
Beezlebot, Roberto, Robot Santa, Flexo. All Unmain. Can anybody think of any OTHER Unmain characters?
Back to the topic. Futurama IS about...6 different storylines. That's what makes it what it is.