When I started this thread, I thought 10 choices may be too many. Then I made my initial list. I had 37 choices. This was pretty hard.
In the end I tried to a) somewhat balance the Mike and Joel episodes (overall, I tend to prefer Mike, but some of the Joel episodes are far too classic to leave out); b) judge episodes based on the combined strength of theatre segments, host segments, classic moments, and repeated viewings; and c) include some "deep cuts" episodes that might otherwise not get any mentions here, yet deserve some recognition. Hence, no Space Mutiny (shock! horror!)
1. Werewolf (Season 9)
This episode can simply do no wrong. Absolutely flawless - the episode, that is. The film is riddled with flaws. (Note that I ultimately felt okay leaving out Space Mutiny because this one is here. They fit into virtually the same mold for me. Plus, I assume Space Mutiny will get a ton of votes without me.)
2. Danger! Death Ray (Season 6)
This almost took number one. It's definitely my favorite of the "deep cuts", and is easily the most under-appreciated episode in the entire run. It's only number 2 because Werewolf has so much more "iconic" material.
3. Pod People (Season 3)
To me, this is the very best of the Joel episodes. It's also probably the best example of an episode that could be great just on the strength of the host segments.
4. The Beast of Yucca Flats (Season 6)
The best (worst?) of the Coleman Francis films (my favorite bad filmmaker from the whole run of the show), great host segments, and TWO phenomenal short films.
5. "Manos" The Hands of Fate (Season 4)
This one is just unavoidable. It's the most iconic of the Joel episodes, and perhaps the most iconic episode of the series. Plus, it really is that funny.
6. Santa Claus (Season 5)
Some people will think it sacrilege, but of the two Christmas episodes, this one is my favorite (though I love Santa Claus Conquers the Martians.) This is just one of the most incredibly "out there" episodes they did, plus the riffing and host segments are top-notch.
7. Mitchell (Season 5)
It marks the great transition from Joel to Mike. Plus it's a movie that's more subtle in its ineptness (it's not sci-fi, horror, fantasy, etc.), making the incredibly funny riffing that much more admirable. Impressive send-off for Joel, and great introduction to Mike.
8. The Final Sacrifice (Season 9)
This one's become a classic for most people, and all of the usual reasons could be mentioned here. However for me, above all else, this episode is on the list because of two words: Mike. Pipper.
9. Future War (Season 10)
Another deep cut, this time from the latest part of the series. It's not mentioned as a classic the way that Manos, Werewolf, Space Mutiny, etc. are, and it really should be. The blatant ineptitude on display here is just fucking mind-numbing, and not in a "we're being tongue-in-cheek here" way like Hobgoblins. These people really thought they were making something good.
10. Warrior of the Lost World (Season 5)
I think I partly put this one here because of my love for old references that I almost get, but not quite. Plus, a handful of all-time best riffs are here.
I would do a list of honorable mentions, but there would be TWENTY SEVEN of them.
Watch the series. It's incredibly hard to find a flat-out bad episode.