I really like Hugo and Jake from the Bible reloaded. Mainly because I have an immature and fucked up sense of humor. But I would really recommend HolyKoolaid or Dark matter 2525. Both actually do videos about the falices of faith and looking at the world in a open minded yet logical veiw.
Some of my favorites have been mentioned, but no one ever seems to mention 43Alley. Extremely disarming good guy next door persona, seemingly ideal for people just beginning to question religion, and those wishing to shore up their own arguments with believers.
Also highly recommended are:
Religion: Why it Can Be Hard to Change Your Mind
How I Gave Up Religion
Which 10 Commandments?
The Living Dinosaur's "Holy Hallucinations" series was pretty good. He's a English scientist of some type that did stylish response videos to creationists. His videos remind me of Comedy Central Roasts but with more robust vocabulary. Too bad he pretty much quit making them.