Some cameos or references to other games I remember out of my head:
Days of the Tentacle: Enter the room with a computer in it, turn it on, and enjoy a game of Maniac Mansion;
MDK 1: In level 3 (the icing-level) when you slide down mountains on you hoverboard, you can collect special Earth Worm Jim powerups for extra lives. The Mad Cow which made its first appearance in Earhworm Jim also appears in this level;
Premiere: Lots of billboards with references to previous Core-games can be found here (Chuck Rock, Heimdall for example);
Super Frog: The horizontal scrolling space-level definitely is a reference to Project X;
Turrican 2: In world 3, level 2 shoot a special power-up and the text 'Katakis lives' will appear. This is of course a reference to Factor 5's earlier work, Katakis);
Zool 1: In a certain level Zool enters a huge arcade cabinet only to play... Zool. He must jump on different buttons to let the Zool-arcade-sprite jump and run.