I like how the article ends with "Tell us about it in the comments!" when Gallery of the Day has no link to the forum thread, and to my knowledge never has. Seriously, for what was once one of the most competently-designed and coded gaming sites out there, things have gotten pretty sad.
The worst port in history has to be Prototype. If you have a CPU with hyperthreading - so, literally any Core i3 or i7, and probably quite a few AMD chips - you cannot launch the game. Period. You have to actually go into the BIOS and disable hyperthreading entirely, which basically turns your CPU into a Core 2 Duo or an i5, respectively. And this isn't something you can toggle on and off at will; you have to cold reboot your system to access this setting.
Other candidates if the list were longer:
BioShock 2, which used 100% of the CPU every second it was running, suffered from texture pop-in on lower-end GPUs, had unreliable peer-to-peer multiplayer that dropped everyone if anyone's connection blipped for even a nanosecond, shoved multiplayer into a separate executable despite not being shipped separately, had no gamepad support, had no equivalent to the console version's radial menus (at least the original had that ugly full-screen weapons-and-plasmids menu), and trying to rebind any keys used in the hacking minigame would make hacking not work. Other than adding gamepad support and fixing the key bindings, none of the above issues were ever fixed, and in fact some patches introduced even more issues like Litte Sisters who didn't talk anymore. What's really damning is that the game ran on the exact same engine as the first game, which had literally none of these issues.
Sonic and Sega All-Stars Racing, which is a racing game with no gamepad support whatsoever. I can't even. Other Sega games eventually patched in support for the 360 pad, but this one never did.