Favorite: E1M3 - First off, I love dark halls; it's Doom ambient music perfection. The map layout is great too, the first area you see after opening the door is very memorable, and so are several other areas such as the nukage pit and blue keycard area. It makes good use of contrast between interior and exterior areas, and has whole chunks of map you might never find without looking for them. Just overall a great map, and it really stands out, even among with other E1 maps.
My runner up would have to be E1M7, for the exact same reasons. The two are very close for me. E1M7 is larger and has better use of 3D space, allowing you to see almost every part of the map near the beginning.
Least Favorite: E2M9 - Fun concept, make the barons fight the cacos, but boring in execution. It seems like it was thrown together at the last second, and the ending key "puzzle" was unbelievably stupid.
Favorite: MAP02 - Tough choice here, I've never really liked Doom 2 as much as the original, so I've played through it far less. There are quite a few maps I like, but I had a much harder time pinning down a favorite. I really like this map though, it has a nice layout and a nice concept. It feels sort of like a real place, in the same way Doom E1 did, which is rare among Doom II maps.
Least Favorite: MAP24 - Again, a tough choice, since there were so many maps I just found to be either boring or irritating (or both) in Doom 2. This one takes the cake on the latter though, I think this sums it up: Vanilla Doom, mouse turning, no novert.