E1M6 is the best in Knee-Deep in the Dead because it is the most complicated and biggest map in that episode, and it also has the biggest monster count on UV and NM: 177 monsters! LMFAO
E2M2 is definitely the best map in The Shores of Hell, and in fact the best in all of Ultimate Doom (even better than all of Doom II and Final Doom, not a single map there that beaten the record of how good that map is) because the crate maze is rather interesting, and you actually get a berserk for the first time, and it's just beyond all comprehension!
E3M4 is the best in Inferno because it has a lot of interesting puzzles, and it has the biggest monster count in all of that episode on UV and NM: 161 monsters!
E4M6 is the best in Thy Flesh Consumed because it really is the interesting version of E4M2 and also has a lot of great things, and it's just overall fun, especially when trying to hide and seek from the cyberdemon popping out of the blue when you get the red key.