A few that comes to mind:
Anathema - Serenades
Not extremely bad, but very boring. "Sleepless" is a fantastic song, but the rest of the album is pretty meh to me. It's not that I don't like Doom or harsh vocals either, but it's not that well executed IMO.
Dream Theater - Systematic Chaos
I really love "In the Presence of Enemies Part 1" which I think is one of the best modern DT-songs. "Constant Motion" is pretty great as well, but the rest of the album is pretty boring to me. I could have also mentioned Octavarium or BCSL, but this album works better in the context, though the others are very uneven to me as well.
Iron Maiden - Virtual XI
On one hand you have "The Clansman" which is not only the best song on the album, but one of the best songs the band has done. On the other hand you have a really bad album. Getting through it is a chore. "The Angel and the Gambler" might have been a good track, if the chorus hadn't been repeated 74 times throughout the song.
Metallica - Death Magnetic
"That Was Just Your Life" starts off the album really well. A great song and I don't mind it at all. The rest of the album is almost impossible to sit through. To me the whole album screams a band doing an album 100% the way the fans would want it to sound, with no energy or quality put into it. There are some other songs that aren't all bad, but I'd rather hear something like Load or ReLoad where the band does whatever they want to, and really put their souls into it, than a soulless album.