I would say that the cover for the album Tuonela from Amorphis is very good since it not only looks neat, but reflects aspects of the album's music very well.
The album Strange Days of the Doors has a great cover. It was designed by William S. Harvey and photographed by Joel Brodsky. Jim Morrison rejected to take part in the cover, nonetheless there is a poster of the band members on the far right end.
I've got a different one there bacobit... only this time it's not nirvana! :P
But seriously now... some of my favorite covers are these:
Queen - The Miracle This cover represents (for me) how closely intwined the four members of Queen were, not only on a musical level, but on a personal level as well... shame the picture 'fell apart' after Freddy died...
Van Halen - Balance This album cover shows a great visual presentation of the album's name, both the 'bad/angry/wild' and the 'good/friendly/calm' sides are represented in it, just like the type of songs on this album are!
Can't think of any more right now, but I'll check in again when I come up with them!
I remember when I first bought that album like 5 years ago... Such a classic. I want to buy it again since I lost it. The album cover was funny to me then since I was in 6th grade.
But anyway, going through my giant album collection, there were two album covers that I liked the most: