Hi! Aurore and I actually answered this question before:

http://fuckyeahjeffannie.tumblr.com/post/21381282433/what-would-you-say-are-the-best-jeff-annie-episodes

In my case Basic Lupine Urology would trump Remedial Chaos Theory right now because what happened there happened all in real life, but it still remains one of my favorites! :)