"The Butcher" abomination found in Black Temple is a reference to The Butcher from Diablo. The item he drops, "Wirt's Other Leg", is a reference to an NPC who lost his leg to The Butcher in Diablo.
One of Illidan's warglaives features a small Pandaren image, the symbol of Samwise Didler.
There is a hydralisk from the Starcraft series hidden in the mission "Daughters of the Moon".
Zerglings from the Starcraft series can be found in the Warcraft III World Editor.
One of the lines said by the Flying Machine unit when dying is "They came from, behind!" before blowing up, a reference to the same line said by Gold Five "Pops" in Star Wars Episode IV: A New Hope.