I think my least favorite is Ghost Reveries, tied with MYAH. GR I just can't stand the cover, the look of the candles, the flames, etc. just turn me off. MYAH is just way too blurry, where it looks like 'Oh, this WAS cool, at somepoint'.
My fave is probably Damnation barely edging out Orchid. The Orchid cover is beautiful in my mind, so sparse yet lush, a black, bare, empty background and exploding through that twin bursts of vibrant colors, which is what Orchid sounds like to me, a dark, bleak base and those organic and emotive twin leads.
Damnation though just immediately establishes the emotion and nuance of the music on the album. Seeing the little girl doll just makes me hear 'Hope Leaves' and 'Windowpane' and 'Ending Credits' all rolled up, and the greyscale monochromatic scheme with the touches of brightness and the more gradual dark shadings perfectly emote the feeling I get from every song.