The darker albums are definitely better, but I have a real soft spot for the quirky pop ones like The Top too. Although obvious, I'd say Disintegration is my favourite as I was sixteen when it came out and it had a big impact on me. I'd heard Charlotte Sometimes a few years before but never knew who it was, it sounded nothing like any of their singles which was all my young ears had heard at the time. Before Disintegration was released I discovered their back catalogue and really got into them, especially the three 17 secs, Faith and Pornography, then Disintegration blew me away. Wish was good but couldn't compete with Disintegration. Wild Mood Swings, meh. Then Bloodflowers was back on form, a really great album.
My favourites change all the time, I know it's only a compilation but the first disc from Join The Dots is absolutely fantastic (I wore out three cassettes of Standing On A Beach), amazing to write songs that good and just throw them away as B sides.