Lori Cardille imitating Rhode's "Choke on 'em" line a little bit in the commentary is worth a big chuckle.
Although it was (probably) not intentional, the scene in the 2008 remake where the infected soldiers charge out, flailing around and firing guns at random. It's hard to imagine any of them were taking the scene seriously.
Before Logan showed the other Scientists Bub, he scolds another ghoul for throwing a table, like a dad disciplining his son. Then shuts the light off. What makes it priceless, is that after the light is shut off, the ghoul's expression looks akin to a puppy wondering what it did wrong. Bonus points for a small rendition of "TheGonk" playing after.
When John makes his speech on why he and Billy insist on being Neutral, he hams it up a bit when he refers to the facility as being one big Tombstone. When that echoes in the cave you can hear a zombie yell back at him.