"Askepios" by the Mars Volta - It pains me that this song came from the same creative force behind De-loused in the Comatorium (which is one of my all-time favorite albums). Once the song gets going, it's actually not all that bad-- but it's all the detours the band takes beforehand that I find hard to swallow. I know Cedric and Omar have a taste for experimenting with how far they can push the music into the realm of noise and voice distortion before they have to steer back into something that seems to have an at least somewhat recognizable structure; even on De-loused they did that. But on De-loused, they pulled it off because their sense of timing and balance was impeccable. On their more recent albums, they occasionally seem to get lost while indulging in their little tangential asides and throw the song off-kilter completely and irrevocably. The second refrain of "What have you brought for my appetite?", with the abrupt stop, the clicking speakers and the rather obnoxious low tone of the distortion of Cedric's voice, always makes me cringe a little.
"Beside You In Time" by Nine Inch Nails - I know of some reviews of With Teeth which have mentioned this one specifically as having a good emotional payoff at the end. I won't deny that it has a good climax, but in my opinion that can't even begin to redeem it for its first three-and-a-half minutes being relentless droning.
"Ddiamondd" by Battles - Yeah... this one I just find completely annoying. I love most of Mirrored (especially "Race: In", "Atlas" and "Tonto"), but I usually skip over this one completely.
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Mediocrity is a petty vice; aspiring to it is a grievous sin.