I just noticed one that I don't think anyone else has before (unlike the previous ones mentioned). It doesn't occur during the actual episode, it's mentioned in a commercial for it. For Ugh (SpongeBob BC), one of the commercials for it is as follows:
Before the dawn of time (roughly 22 minutes before), evidence suggests me that life began...to giggle. *Spongebob and Patrick laugh* Fossil. Your. Seatbelts. The evolution is about to begin. *shows a Spongebob timeline, from caveman to modern Spongebob* Spongebob Goes Prehistoric.
SpongeBob BC is a special, so it's 22 minutes, instead of 11. Notice the "roughly 22 minutes before" part. ^_^