Only the base damage; although with bows, arrow damage is affected as well.
Source: http://www.uesp.net/wiki/Skyrim:Sneak (the sentence you want is under the second table)
All tests performed on Devin Mallory in The Ragged Flagon (by the miracle of quicksave, no Devin Mallorys were permanently harmed by these tests):
Poison Tests
Test I: Control
Glass Bow, base damage = 29
Steel Arrow, base damage = 10
Sneak attack x2.0 damage = 72.04 damage (I assume reduced from 78 by armor, I have no idea what the math on that looks like)
Test II: Poison
Glass Bow, base damage = 29
Steel Arrow, base damage = 10 Weak Poison, damage = 15
Sneak attack x2.0 damage = 85.69 damage (again, I assume damage was reduced by armor, but since the poison didn't even do its full damage, it's definitely not doubled by the sneak attack)
Enchantment Tests (as suggested by Fizz):
Test I: Control
Hunter's Bow, base damage = 8
Ancient Nord Arrow, base damage = 10
Sneak attack x2.0 damage = 15.46 damage
Test II: Enchantment
Hunter's Bow of Chills, base damage = 8, frost damage = 6
Ancient Nord Arrow, base damage = 10
Sneak attack x2.0 damage = 35.6 damage
Based on that, I'd say shock/ice/fire enchantments are affected by the sneak attack bonus. If someone feels like figuring out Devin's armor and doing some math, feel free!