Oh I'd say there were many more than three. I can recall these from my viewing:

• The startup sound
• The Hello Dolly player
• The skittering second gen. ADB mouse in the trash room
• The Axiom's voice
• EVE, but she hardly needs be mentioned

I've heard there's a specific scene that looks an awful lot like 10.5's default nebula desktop picture, but I didn't catch that one.