Season 1
Best: I Dream of Feeny
Worst: Grandma Was A Rolling Stone

Season 2
Best: Sister Theresa
Worst: Cyrano

Season 3
Best: City Slackers
Worst: Train of Fools

Season 4
Best: B & B's B 'N B
Worst: Singled Out

Season 5
Best: Raging Cory
Worst: No Guts, No Cory

Season 6
Best: Friendly Persuasion
Worst: And In Case I Don't See Ya

Season 7
Best: Brotherly Shove
Worst: As Time Goes By

Season 1
Best: The Fugitive
Worst: Boys II Mensa

Season 2
Best: Sister Theresa
Worst: Who's Afraid of Cory Wolf?

Season 3
Best: New Friends and Old
Worst: I Never Sang For My Legal Guardian

Season 4
Best: You Can Go Home Again
Worst: An Affair to Forget

Season 5
Best: Raging Cory
Worst: Heartbreak Cory

Season 6
Best: Better Than the Average Cory
Worst: And in Case I Don't See Ya...

Season 7
Best: Family Trees
Worst: How Cory and Topanga Got Their Groove Back

This is a toughie but I'll give it a try:

season 1:
best: Cory's Alternative Friends (my 2nd favorite episode of the entire series)
worst: Grandma Was a Rolling Stone

season 2:
best: Wake Up, Little Cory (so many good episodes this season)
worst: Me and Mr. Joad

season 3:
best: The Grass is Always Greener (my favorite episode of the entire series)
worst: Stormy Weather

season 4:
best: Wheels
worst: Janitor Dad

season 5:
best: And Then There Was Shawn
worst: No Guts, No Cory

season 6:
best: Resurrection
worst: Friendly Persuasion

I haven't watched season 7 in a long time and these episodes are not fresh on my mind so I will not include it.