As usual, Spoilers Off for moment pages. So proceed with caution. You Have Been Warned

How does The Second Encounter begin? With the Sirian ship crashing upon... Colliding with a bus full of Croteam employees.^note
After getting the Skull at the end of one of the earliest levels, Sam cannot resist the temptation to do the obligatory literary reference:
"To be or not to be... that is a serious question."
Two levels later, Sam spots a statue depicting a snake with a head on both ends and dispenses some wisdom of his own.
"...huh. They always said two heads are better than one... but how does it fart?"
The secret watcher turns out to be... A giant beheaded kamikaze.
"Secret mighty kamikaze has been activated!"
There are several rooms in the game which have gravity fields that propel enemy mooks (and the player) around from wall to wall. The game also supports doppler shifting of sounds. The rooms are full of kamikaze bombers. You can see where this is going.
"AAAAAAAAAAAAaaaaaaaaaaaaaaaaaaaaaaaAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"

Funny / Serious Sam: The Second Encounter