File 06 was easily my favorite one. The forced stealth at the beginning was kind of a pain to get through, especially with me who likes to scour every nook and cranny of every part of each level, but everything after that was glorious. The whole story around Sector V, Kyle's boss fight and his design, the merging with the Astral Plane and the boss battle against the Hommunculus, they were all AMAZING.
I honestly don't know if I have a least favorite file. Probably File 08; I didn't dislike it, but the traffic jam puzzle blue case was hell for me because I am very bad at those types of puzzles, and I also had a big issue with getting locked off from parts of the level I was still trying to explore and being forced into a timed mission.