I think the plot order would be this:
Beach Party Mummy
A Beautiful Mine
Sorry, Wrong Era
Retroville 9/Grumpy Young Men
Operation: Rescue Jet Fusion
Nightmare in Retroville
Monster Hunt/Jimmy for President
Holly Jolly Jimmy
Love Potion 976/J
Return of the Nanobots - ‘Cindy sings the body electric’ would likely be after Love potion
Maternotron Knows Best/Send in the Clones - again just after love potion
Sheen’s Brain
The Great Egg Heist/The Feud
Out, Darn Spotlight
Foul Bull/The Science Fair Affair
The Junkman Cometh
Men at Work
The Mighty Wheezers/Billion Dollar Boy
Attack of the Twonkies
Win, Loose and Kaboom
Lights, Camera, Danger
Fundemonium
Jimmy Goes to College
Stranded
N-Men
The Tomorrow Boys
My Big Fat Spy Wedding
Who’s Your Mommy/Clash of the Cousins - this being aired after LoV is just lol, Jimmy would have already known Baby Eddie was the Evil One.
Crouching Jimmy, Hidden Sheen
The Incredible Shrinking Town
The Trouble with Clones
One of Us/Vanishing Act
The Evil Beneath/Carl Wheezer, Boy Genius
Who Framed Jimmy Neutron/Flippy
Best in Show - Cindy still reluctant to be nice to Jimmy, needs to be before King of Mars
El Magnifico
How to Sink a Sub
— Would’ve been nice to have an inbetween J/C in preparation for the King Of Mars dump here if they had the time, has to be after Best in Show tho I think. —
King of Mars
Lady Sings the News - Has to be directly after King of Mars for the flirting to make any sense
The League of Villains - has to be after King of Mars because of Eustace.
Non-Canon but if they were ordered
JTPH1 comes somewhere in Season 2
JTPH2 comes after League of Villians - Calamitious has escaped from the Crustaceous era
JTPH3 comes after again