I looked up Penetrating Strike in Dungeonscape.
Does Craven apply to this damage, as it doesn't call the damage sneak attack.
I have no idea, it's not an issue the writers of Dungeonscape anticipated, since sneak attack is normally only dice damage. I'd ask your DM. A reasonable middle ground between getting or not getting it is having it halved, just like your SA dice.
In any case, Penetrating Strike is mostly a stop gap when all else fails. Ideally, you'll be angling towards a +3 weapon (the minimum enhancement a weapon needs to be able to apply a greater augment crystal to it), and a greater truedeath crystal and greater demolition crystal. The former is 10,000 gp and among other things lets you SA undead. The latter is 6000 gp and lets you SA constructs. Together, they let you ignore about half of the SA immune stuff in the game.
If you're not familiar with them, augment crystals were introduced in Magic Item Compendium. You basically have one "slot" on any weapon, armor, or shield that can hold one. Attaching or removing them is a move action, so swapping them in combat IS an option when needed. They're basically like magic arms/armor bonuses that are easily transferable between gear and purposely designed to give you more customization.
EDIT: Unless you're doing Zhentarim and/or Dungeoncrasher Fighter, I recommend not going beyond level 2 in Fighter. If you feel the absolute need for Melee Weapon Mastery, take the bare minimum Fighter levels that requires and get out. Dungeoncrasher Fighter is in Dungeonscape. Zhentarim is located in a small downloadable pdf
here. It makes Intimidate a very useful skill, and actually gives all of its benefits for FREE.