Most of them in a fast montage.
The 500th episode, At Long Last Leave, paid homage to Kill the Alligator and Run, Cape Feare, Kamp Krusty, and The Call of the Simpsons. Excellent.
With 500 episodes of The Simpsons, it is hard for me to put the episodes after the 200th episode in any meaningful context. I have 269 episodes on DVD. I still haven’t gotten around to purchasing the 13th and 14th season DVD sets.
Dont Fear the Roofer is the last episode that I can put in context. It is in the 16th season. It’s from 2005. It guest stars Ray Romano. It is the 351th episode. I liked how the writers, producers, and everyone took a different turn with Homer meeting a roofer and developing a friendship with him. I really liked how, in classic Simpsons fashion, the friendship plot had a twist.
For some reason, I really like Simpsons episodes that have a plot with a twist. So, for that reason, my choice of My Sister, My Sitter, as my favorite Simpsons episode, after watching 500 episodes, stands.
[slight hijack]
Reading these is both cool and sad. Cool thinking back so long, sad thinking how much the show has declined in the last ten seasons. Shell of its former self really. 
What’s really strange for me, anyone who’s read my posts knows that I used to absolutely hate Family Guy. I still hate the first generation of them, before it was first canceled. But I watch a lot of Adult Swim so over the past few years I’ve inevitably caught a newer FG here & there and, begrudgingly, started to like them.
And now when I think about it, I hate the older Family Guys because they were like the newer Simpsons: Too schticky, flat 2D characters, no character development, no story logic, no whit or intelligence etc. And now the opposite is also true. I like the newer FGs for the same reasons I loved the older Simpsons: More believable characters, more whit, more meta-humor etc.
Cue Comic Book Guy voice: "What is this, bizzaro-world?!"
[/hijack]
Oh, and here’s another vote for Homer’s Enemy (and it was my favorite before I read it was Groening’s too!)
“Oh look, high voltage power lines! Well I don’t need safety gloves, because I’m Homer Simp-BZZZZZ”
I’m a sap. Lisa on Ice
I’ve always loved Who Shot Mr. Burns? If I have to pick one, I’d pick part 1. It may not be the funniest episode, but its very well written
I didn’t see the 500th episode (no access to TV), but I was curious enough to look it up on Wikipedia… the episode actually ends with the entire city relocating? Back in my day, that was the exact ending of the 200th episode!
I believe that I’m in the minority, but I’ve always loved A Star is Burns. Lots of great lines…
“Boo-urns!”
That’s why I wrote in my previous post, “it is hard for me to put the episodes after the 200th episode in any meaningful context”. 
It was so wonderful, I cried a little.
Homer in space. Eating the loose potato chips to “The Blue Danube.” Smashing open the ant farm, as the ants click to each other, “Freedom! Horrible, horrible freedom!”
Yeah, Homer in Space would be a close second for me, considering it’s where I took my screen name from!
“…and I for one welcome our new insect overlords…”
The one where where people throw ducks at balloons and nothing’s the way it seems.
The Irish episode, where Bart and Homer nearly become Catholics and Marge dreams what Catholic Heaven is like.
I haven’t watched the Simpsons for years, didn’t realise it was still in production.
I gave up on watching The Simpsons a few years back, but the TV at work happened to be tuned to the 500th episode. I liked it a lot more than I thought I would, but the way the show rushed to hit the reset button at the end kind of reminded me why I gave up in the first place.