I'm going to pick on two favourite albums here:
Beck - Sea Change: Paper Tiger... Just totally kills the mood and doesn't fit with everything that follows. One of the few albums where I always skip a song.
And the following only applies now with hindsight:
The Future Sound of London - Dead Cities: We Have Explosive... This was of course the big hit. It hasn't aged well though, and it stands out as incredibly harsh against the rest of the album. I typically don't skip it but I'm basically waiting for it to end the second it starts, and right when you think it's gone on long enough, it starts back up again.
Speaking of FSOL, their new album, Rituals E7.001, opens with perhaps the worst song they've ever written, but goes on to be otherwise excellent. I tend to skip it maybe 50% of the time, depending on my patience for hippie psychedelica at the moment.