Wyldstyle makes a comment about the Wicked Witch “defying gravity.” That is also the title of a song in the musical Wicked.
In the mission “GLaD to See You,” H.A.L. 9000 from 2001: A Space Odyssey appears and speaks with GLaDOS.
After you beat the Portal levels, you’ll enter a storage room filled with boxes marked with the logo of Black Mesa, from the Half-Life series (which shares a universe with the Portal series).
In certain underwater areas, such as in the Lord of the Rings world, you can find two fish that resemble Marlin (or possibly Nemo) and Dory from the Finding Nemo movies.
In the Mission: Impossible level, when you save Benji (voiced by Simon Pegg), he comments on his new plan to “have a cup of tea and wait for all this blow over.” This is the same plan Simon Pegg’s character suggests in the movie Shaun of the Dead.