Dark Souls still doesn't seem like a bad port to me. Extremely straightforward direct port, though, but not as BAD as some others. Not particularly good either but the game sure is excellent (though it sure as hell is a million times better on PC than the console version once you install DSFix... too bad about the GFWL, though)
Regardless,..
GTAIV is up there as a pretty damn awful port, performance-wise. Sure, if you can run it well you can get some pretty damn awesome mods.
Borderlands is another one, which blows my mind because it performs so much worse than Borderlands 2 despite being a technically inferior game. Or is my computer THAT bad? I also remember hearing that BL1 had some awful mouse smoothing early on but they changed it with patches. Like, who even thought that forced mouse smoothing was a good idea for a FPS!?
The recent CoD: Ghosts sounds like an awful port, with arbitrary system requirements that make no sense considering it barely even looks much better than BlOps2. I didn't care much for it, but the status of the PC version of Ghosts really shows that Infinity Ward and Activision don't care. The requirements seem inflated so that people think it really requires a much better machine than BF4...