You know, the ending of Perdido Street Station is one of those that will stick with me pretty much the rest of my life, I think. It was brutal, but it was also so spot-on perfect for that book. That said - I imagine when I reread these books, I'll probably reread "The Scar" first. Everything about it is so so so cool from all the stuff you listed (The Possible Sword, Armada, the Avanc) to the Brucolac, the Lovers, Uther Doul, and the Scar itself. Yeesh.
I think I'll reread The Scar first. (Although, I duno. I really could go for rereading both of them...)