Zealous Programming: One of your soldier types can activate this ability to increase stats, speed, attck for a limited time blah blah, but you temporarily lose control over them.
Heightened Sensory Equipment: Your command base sends a signal to all your Pathfinder type units which increases sight range.
Resistance Programming: This upgrade adds a 15% resistance to all your machines against human hacks. Also boosts mana.
Diehard Protocol: Temporarily raises defense by 75%, but slows attacks by 25% for 30 seconds.
Secondary Initiative: Gives machines a 10% chance to resist EMP shockwaves, preventing them from shutting down.
Bite my Shiny Metal Ass: Taunt ability. 'Nuff said.

Also sounds like a cheat code.
Balance the Equation: Infiltrator type units can cast this on an enemy unit, they will then take on the attributes and stats of that unit. (If possible, this will allow them to sneak into enemy base unmolested, save for detectors. Dark Reign style.)
Hardcode: Your command centre thingy can channel this ability for a short time. Raises attack damage, movement speed and accuracy of all machines by 25% for a short time, but decreases armour by 25%.
Improved Insulation: Upgrade. Renders machines immune to low levels of weather effects.
Programming Be Damned: I actually have no idea what this would be. I just liked the name. Maybe a Terran hack ability. I'd imagine that whatever the case, the machine would spaz out and attack everything that comes near at an increased attack damage/rate, or it could be a Kaboom ability. The machine suicides itself into the enemy.
The Code of Life: Spawn ability?
Cold Rage: Berzerk type ability.
Machine Logic: Increase in efficiency, building/workers work faster.
The Matrix: Couldn't resist it. Short term ability that hooks the machine directly into the command matrix, creates a command aura that boosts energy and ability stats, and gives a Brilliance type boost to surrounding allies.
Okay, I don't know how much this box will let me write, so I'll stop there.