I quibbled a bit, actually a lot, with their list of MST3K episodes, but the only complaint I have about the AVClub’s Star Trek list is the inclusion of the Season 3 episode “Spock’s Brain”, an episode I haven’t seen since high school and haven’t missed. If Zach Handlen were to compose a list of episodes that we could do without, “Spock’s Brain” could assume its rightful place.
You’d be better served by any of the episodes Zach Handlen lists in the second ten. My favorites in that group would be “Errand of Mercy” and “The Doomsday Machine”. (They really should have piled on more Norman Spinrad during the series.)