Big Lipped Alligator Moment: The fight with the GLaDOS in the final chapter, it happens suddenly when John is fighting when he is dragged into the chamber and then it is forgotten as John Freeman goes to continue his assault with the Combine like the event never occurred after GLaDOS is destroyed.
Zombie goasts becomes more hilarious when you watch Panty & Stocking with Garterbelt, specifically, episode 8's first segment "...Of the Dead" features... Zombified Ghosts.
At some point during Free Man, John Freeman goes on killing Combines with bear hands! (This was even noted with a clever Visual Pun on Djy1991's machinima) Some years later, a new pair of "boxing gloves" for the Heavy were added into Team Fortress 2: They are a pair of severed bear hands!
In the Djy1991 adaptation of Free Man, they added in a scene that lasts from 6:12 to 11:38, where they deviate from the original, making John Freeman into a badass god figure by showing him fighting through a number of memetastic locales. While it was praised by some viewers, others felt that it added nothing to the video.
Within that segment, while most of the fighting was more or less in line with the rest of the story and John Freeman's larger-than-life image, there is an indisputable BLAM when the G-Man, who has a Hitler mustache, shows up and kicks John Freeman into the sky, before turning into Saxton Hale. John Freeman goes flying over various locales from assorted Source-based games such as cp_gravelpit, ctf_convoy_v2 and gm_bigcity, ultimately landing in GLaDOS's main chamber, where John Freeman gets into a one-sided argument with her, blows her up and arrives back at the Citadel just in time to see the humens at safe place before the Citadel explods.
"the countrysides were nice and the plants were singing and the birds and the sun was almost down from the top of the sky."