Any damage other than 'precision' damage (Sneak Attack, Skirmish, etc) Or special enhancements (Vicious, Merciful, Flaming, etc).
For the most complicated example, lets use this:
say you have a +1 Flaming Longsword, Weapon Specialization, 1d6 sneak attack, and a strength of 18.
Your normal longsword damage is 1d8+1d6+7, with an additional 1d6 when you sneak attack. If you roll a crit, the 1d8 is doubled, as is the +7. the 1d6 fire and the 1d6 sneak attack are not.
Make sense?