Groening/Brooks/Simon: Lisa's Substitute
This episode contained the best use of the show's emotional core IMO. Mr. Bergstrom was a very good "eccentric, yet wise" type of character and the scene with the goodbye at the train station remains one of my picks for some of the saddest cartoon moments (that line “That’s the problem with being middle class, anybody who really cares will abandon you for those who need it more.” Powerful stuff.) The subplot also provided some great comic relief for the serious main plot. Definite top 5 material.
Jean/Reiss: Radio Bart
A great show of the type of humor that was a staple of early seasons. Bart playing with the label maker and microphone was a lot of fun and it's also chock full of great Homer material ("Aww, there's only one beer left and it's Bart's.", the scene where he grabs a gun because he thinks aliens are attacking). Not to mention, the whole "well" thing, while a bit over the top, was very captivating nonetheless.
Mirkin: Lemon of Troy
My favorite episode of the series. The caper plot was very well done and I loved how realistically the kids were portrayed here. I wish this episode's kid portrayal was used in other episodes - Zombie Simpsons or otherwise, but what are you going to do? In addition to the plot keeping you on the edge of your seat, there are some great and memorable lines and gags in every single scene.
Oakley/Weinstein: Homer vs. The 18th Amendment
This was a tough one. O&W are my favorite showrunners, so there are tons of episodes to choose from, but I chose this. Like Lemon of Troy, the plot is very suspenseful and there are also some memorable moments in every scene, but I have to praise Oakley and Weinstein for showing Homer's cunning and genius side without turning him into a jerk. Just think how terrible this episode would be if this was a regrettable Mike Scully adventure! Then again, that could be said about a lot of episodes, but I think this shows that.
Scully: Lisa Gets an A
Best post-classic episode without a doubt. This episode and Treehouse of Horror 9 are the ONLY post-season 9 episodes I could see fitting into the classic era seamlessly. The humor was in the wittier classic era vein, the characters weren't annoying (except for a few scenes, such as Homer shoving Lisa into a freezer or guzzling beer through a hole he made), and I genuinely cared for Lisa in this episode. Very well done.
Jean: Half-Decent Proposal
Really, it's a tie between this and Eternal Moonshine, but I picked HDP because the plot felt like something that could have been done in the classic era and it was just as captivating as any "big" plot from back then. The episode its self was far from classic, but by modern Simpsons standards, this was incredible.