There are, of course, others that do the same for other reasons, but there is a common thread running through one episode from each of Moonlighting's first three seasons that really makes them stand out to me as something special.
The Next Murder You Hear
Witness for the Execution
Blonde on Blonde
I could elaborate, but suffice it to say that these all feature dark and stormy nights, a heavy dose of atmosphere, and emotions running high. They are simply classic 10/10 episodes in my book, and they would make a perfect late night (storm preferred but not required) marathon.