Looney Tunes (An entire episode was dedicated to the Coyote and Road Runner). That show had numerous other references too, including an appearance of the Enterprise itself.
Dr Strangelove or How I Stopped Worrying and Learned to Love the Bomb. (Dear John and Hi There for instance)
Dark Crystal
Dracula
Star Wars
There are many many more. The entire show was one big reference to something else.
One of the more esoteric Star Trek references was the aliens urinating. In Star Trek, no one pees. The only time any time of shower/rest room is shown in the entire franchise is in ST:TMP when the Ilia drone appears on the Enterprise. There might be a scene in ST:TOS where Kirk comes out of a door with wet hair and a towel around his shoulders, but that's it.
About the only franchise/movie that I cannot think of a reference in Farscape is Stargate.