Favorites: Wolf3D Episode 6 and the original Spear of Destiny (yes I know the later might spike some controversy, but it is clearly one of my favorites)
Least favorites: That's easy. Return to Danger and Ultimate Challenge. Nothing else comes close.
E1 likes: The episode that started an entire genre of gaming. It's freeware. The first level I know like the back of my hand. Most of the levels take up relatively large map space. The secret level is one of my favorite Wolf3D secret levels.
E1 Dislikes: It is rather predictable. You always have to get one key somewhere in the map and then the exit is somewhere else. There isn't a lot of variety. And the levels that aren't predominately grey shouldn't have had grey skies anyways.
E2 likes: Completely different from any of the other six episodes. I also enjoyed most of the level design.
E2 dislikes: E2L8 pushwall maze is way past redundant and forget about 100% secrets. E2L7 also seems redundant unless ID wanted to put in the gimmick of essentially being a "second secret level". The Dr. Schabbs fight is my least favorite in the game.
E3 likes: You're after Hitler, the madman behind it all! It's the heart of the game, that's obvious. And most of the level design, again, fits my liking. I like the Pacman secret level even if it's just a gimmick and wow did they make it not easy to find (at least relevant to back in the day).
E3 dislikes: Either route in E3L7 is a bit brief in terms of action IMO. And the designs still aren't true top notch.
E4 likes: Some large, extensive levels just as I like them served. Particularly E4L5, E4L6, E4L8. E4L1 I have no problems with as an introduction either. And the way to properly get the keys on E4L9 is clever, even if nowadays anyone would see the trap coming.
E4 dislikes: I don't care for the quick exiting opportunity in E4L2, E4L3, E4L4, and E4L7. I think the secret level should give a path where 100% treasures is doable without having to confront all 75 Officers. And the fact that you can completely seal off the key on E4L7, even though it's more common to just fire at start and kill a guard in the door.
E5 likes: A lot of more compact designs which don't bother me at all. The huge fight against guards after the boss is a perfect foray to Episode 6.
E5 dislikes: The boss is a step back from previous ones in terms of difficulty. I don't care much for the secret level.
E6 likes: A huge majority of things. Large levels. Very challenging. Mazey, but not in a way that discombobulated me. E6L8 is probably my favorite ID Software level including SoD. So long, and so tough, what a penultimate level. The music for the secret level rocks!
E6 dislikes: Mostly just in E6L2 that the ENTIRE map is one texture and the vast majority is a maze that's not hard to get lost in. I think E6L10 should have required exploring of two of the areas. Keep the bosses in the north and south quadrants, don't change the east quadrant (the player does not have to explore it at all), but put a silver key in the west quadrant and require both keys for the elevator.
SoD likes: Mostly extensive levels. A few extra features, even though not much. I came here for more quality Wolfenstein times, not necessarily much new,. and that's what I get!
SoD dislikes: Maybe they could have enhanced it just slightly further, but I'm not big on that since like I said all I am looking for is more Wolf3D. I think putting the two keys on Level 2 right next to each other is a waste; I'd rather have had more of the map mandatory to explore. If it's possible to block the winning solution on Level 20 without knowing immediately, then that as well.
RtD likes: Virtually nothing.
RtD extreme dislikes: Some of the enemy placement and level design is just total tripe.
RtD dislikes: Cheap new graphics/sounds/sprites. Even the better designs struggle to make mediocre. Too many pushwalls are marked yet a couple mandatory ones aren't. Basically everything except my extreme dislike.
UC likes: Some of the level design at least makes some sense. Going to the Doom universe at the end.
UC dislikes: Still a lot of pretty poor designs, and everything else I disliked with RtD as well since besides some level designs, all the other characteristics carry right on over.
If RtD and UC were Spear Resurrection and EoD officially, or if those two games were just official in some way, they would easily be my two favorites of them all. Alas they aren't official chapters since ID/FormGen had no involvement.