Since you mentioned the ladder bosses I just feel like mentioning the mother of all ladder bosses from MGS3 tough it may not have been a FPS game, the sheer length of it is more than enough for it to qualify.

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Jared, I know how you feel about the Helghast thing. I did the exact same thing on a freddiewong video, and my friends blew my ass out about it. I told them sorry, jeez, I didn't play Half-Life yet.

Whale Juice: For when you're at Half-Life. [=)]