My favorite is also an easter egg, from E-Mail #50.
"
I’m also partial to E-Mail #68 Caper.
I got mad at the Cheat . . . For bungling the Jumble Caper . . . I hope I don’t see his name in the paper . . . In the obituaries . . . Because that would mean that he’s dead! The Cheat is not dead . . . I’m so glad the Cheat is not dead! The Cheat is not dead . . .
My favorite is also an easter egg, from E-Mail #50.
**Dear Sir Strong Bad. Stop. How do manage the telegramaphone whilst wearing gentleman’s sport gloves? Stop.
signed, Sir Elsington Hallstingdingdingsworth**
I’m also partial to E-Mail #68 Caper.
I got mad at The Cheat . . . For bungling the Jumble Caper . . . I hope I don’t see his name in the paper . . . In the obituaries . . . Because that would mean that he’s dead! The Cheat is not dead . . . I’m so glad the Cheat is not dead! The Cheat is not dead . . .
It is so Monster Truck. The Cheat game egg at the end is great plus you get an autographed photo of Limozeen. What’s not to like?
And it wouldn’t hurt to soup up your name a bit, Kyle. Like … Kyle “The Yellow Dart” Smith.
Another vote for Trevor the Vampire. I’m also quite fond of “Sweden”
And the classic: fhqwghgads
Since I can’t vote for something that isn’t a Strong Bad email, that rules out Fluffy Puff Marshmallows (“Before I drink something, often times I eat something too”) and Welcome Speech (“It’s dot com”). And it rules out Metro Pops Interview (“Well, if you take a look at my resume, you will see I have a lot of experience in many related fields”). And it rules out Meet Marshie (“I hate that freakin’ marshmallow”).
Drat.
I guess I’ll vote for Japanese Cartoon (“And for some reason, I’ve got blue hair”), Interview (“I was raaaaa-aaised by a cup of co-ooffeeee”), and Island (“Hey, Strong Bad, is there ice cream yet?”).
FISH
P.S. I have a Homsar shirt. It said “raised by a cup of coffee” on the back. I’m going to get a The Cheat shirt as soon as they’re back in stock. 
“Did you take some of my pills again?”
#36 - guitar - “and the dragon comes in the NIIIIIIIIIIIIIIIIGGHH [collapses]”
#43 - little questions - “I’m’ve was to make football often times. Play? Know.”
#53 - comic - “Kristen, you look burnt … or DEAD”
#62 - interview - “I was raised by a cup of coffee.”
#69 - personal favorites - simply because of the intro (“Whoa. That ruled.”)
But I really don’t think there’s one (or even more than one) “best” email. It’s all the little things in each email, and the staying up late every Sunday (sunday! someday!) night waiting for the new one that makes it all so great.