I tried to make a top 10 list, but that proved to be harder than I thought. I just started listing them from earliest on and got to 13, which seemed like a fitting number for a Supernatural list.
1. 1-1 Pilot: As pilots go, I'm certain there are better one's out there. However, I had to include it because its Genesis, the way we met the Winchesters and in a lot of ways, it tells us everything we ever needed to know. Dean is a smartass, but deeply messed up. Sam is striving to be normal, but deeply messed up. Daddy Winchester, though absent in this episode is just deeply messed up.
2. 2-1 In My Time of Dying: Season one had some good moments, but this is when the show comes into its own. Great performances here from Ackles, Padalecki, and Morgan as Daddy Winchester sacrifices himself to bring Dean back. The concept of selling your soul would also become a cornerstone of the show.
3. 2-22 All Hell Breaks Loose, Part II: I still cry every time Dean is talking to Sam's dead body and I still cheer every time Dean shoots the Yellow Eyed Demon after an assist from briefly corporeal Daddy Winchester. Also, its the episode I always remember when I hear 'Carry On, My Wayward Son' by Kansas.
4. 3-8 A Very Supernatural Christmas: This episode is both hilarious and heartbreaking, as well as more than a little gory. Its the first time that we glimpse the brothers' childhood, and it hurts my heart, y'all. Also, I just love a good Christmas episode, no matter the show.
5. 3-11 Mystery Spot: The trickster is at it again, as Sam experiences a macabre groundhogs day, watching Dean die over and over again in a myriad of ways. Its funny all the way through, but the ending isn't, as we see how Sam reacts to Dean being really dead, a portent of things to come.
6. 4-1 Lazarus Rising: This episode sets the tone for what'll be two seasons of Apocalypse, and it introduces Castiel, angel extraordinaire.
7. 4-6 Yellow Fever: Wussy Dean is the most hysterical thing ever: running from the Yorkie, screaming like a girl, manning the flashlight. Also, before the credits, the video of Jensen Ackles lip-syncing 'Eye of the Tiger' is my most epic video ever.
8. 4-13 After School Special: Dean as a gym coach in tiny, tiny shorts? Yes, please, and thank you. Plus we get an insight into the school days of the Winchester boys.
9. 4-17 Its a Terrible Life: Sam and Dean caught in an angel induced illusion where they are strangers who work in the same corporation, banding together to defeat an angry spirit. The many jokes that long time fans will get are what makes this episode great.
10. 4-18 The Monster at the End of this Book: The Winchesters find out that there's a book series chronicling the last couple years. I love the prophet Chuck and the brothers learning about the crazy fandom, including Wincest!
11. 4-22 Lucifer Rising: The shot at the end of Dean grabbing onto Sam when they realize Lucifer is coming makes this whole episode worth it. Poor, poor Winchesters.
12. 5-8 Changing Channels: Hilarity from beginning to end as the brothers are trapped in different television universes. My favorite is the crime procedural with both brothers doing their best Caruso. Also love Sam as the Impala.
13. 5-10 Abandon All Hope: *sob* That's really all I can do or say here. Sad, but beautiful.