My favourite parts in the architecture were more of those between the levels rather than in them - the way that first 'Poor Yorick' and 'Confound Delivery' and then 'Where Some Rarely Go' and 'Thing What Kicks' are so brilliantly joined together. They were always some of my favourite levels.
Otherwise I always liked the level architecture of 'Kill Your Television' - the wonderful trick of going underwater and coming up somewhere totally different is one of my favourites, and it was also important on 'Thing What Kicks' and kept me guessing for a while the first time around!