The crouch stab deals the same amount of damage as the previous sword-like attack, no matter what attack was previously conducted. For example, one could jumpslash with the Biggoron's Sword, pause and equip the Master Sword, and then continue to deal Biggoron's Sword jumpslash damage by crouch stabbing with the Master Sword.
This is often used to a great advantage by "storing" the damage amount dealt by a more powerful but slower attack (usually a jumpslash) and using the much faster power crouch stab instead for increased damage output.
The power crouch stab can be combined with ISG to deal massive amounts of damage every frame.
When Link enters a new scene, the default damage dealt by a crouch stab with any weapon is 1, or the same amount of damage dealt from a slash from the Kokiri Sword. Yes, a crouch stab with the Biggoron's Sword will take 4 hits to kill a blue Tektite if it is the first attack used upon entering the scene!
The special properties of the last attack are carried over with the power crouch stab, such as the Megaton Hammer's ability to destroy boulders, or the Master Sword's ability to deal more damage to Ganon. For example, if you swing the Megaton Hammer, then switch to the Master Sword, Link will be able to destroy boulders with it by crouch stabbing them.
If your previous attack is a Spin Attack, the power crouch stab will only deal slash-strength damage, even when using a charged (orange) spin attack.