If I was to make a list like this, as much as I like the show from the beginning up to around season 16, I think my list would be mostly seasons 6-9. Those were the seasons which came out when I was about 8-12 years old, and the point at which I really began to appreciate the show as something greater than everything else I was watching. On top of that, I think those seasons hit me at just the right point of my childhood to actually contribute significantly in shaping my sense of humour, so when I return to those seasons, the tone of the show continues to strike the perfect chord with me.
My two default answers for favourite episode are the Frank Grimes one (late season 8) and Homer Simpson vs. New York (early season 9). I don't know my way around the seasons that well, but just glancing at a list of episode names in 6-9, I immediately recognise as brilliant ones that would be in contention for my Top 20: You Only Move Twice, King Size Homer, Hurricane Neddy, Homer the Smithers, Lisa the Iconoclast, Mountain of Madness, Bart Carny, Bart's Comet, Homie the Clown, Bart vs. Australia, Lemon of Troy, Summer of 4 Ft 2... you get my point.
A few favourites outside that period (again, just browsing episode titles and going on instant feelings towards the episodes) are Bart’s Dog Gets an F, Itchy and Scratchy: The Movie, Rosebud, Treehouse of Horror V (the Shinning one), E I E I D’oh, and my late inclusion would have to be Don’t Fear the Roofer.