Negative energy is associated with the Neg Energy Plane. It typically is associated with undead (who "live" via Neg Energy) and evil Clerics. Inflict spells are negative energy.
No, negative energy and ability damage/drain are not the same thing, even though some monsters do both. So, a touch attack by a wraith does 1d6 points of negative energy damage to your hit point total, but also (with a separate d6 roll) Con drain.
I believe that all undead who drain you in any way are supposed to use negative energy to do so. (usually)
Not sure of any specific game rules that reference that, but i believe that is what is intended, and why undead are immune to effects like them
Not subject to nonlethal damage, ability drain, or energy drain. Immune to damage to its physical ability scores (Constitution, Dexterity, and Strength), as well as to exhaustion and fatigue effects.
Thematically that 'makes sense,' RAW it doesn't figure into the rules, unless the damage is typed (in the description) there is no rule saying the default is negative energy.
For example, lets say a character has an item that grants immunity from negative energy effects. That character gets hit by a STR drain/damage attack from some wispy undead creature. The damage happens as the STR drain/damage isn't actually classified as a negative energy attack.