List of Commanders of all the star wars battalions on Empire WAR! commend the star wars Wiki.
501st Legion: Led by me Twgxslugger (Anakin Skywalker) Captain Rex: (I don't know)
212th Attack Battalion: Led By Obi-Wan Kenobi (Mr_cookiesmurf) Commander Cody: M4rine_semperfi
41st Elite Corps: Jedi Master Luminara Unduili (don't know) Commander Gree: Tobberz
Delta Squad: Boss: Tim Scorch: Robwookie Fixer: Only_God Sev: Rikumaru
Clone Force 99: Led by Clone Sergeant Hunter members: CrossHair, Tech, Wrecker
Clone Pilots: all of them are Available
Clone Admirals: Admiral Yularn (DS_Nine)
Coruscant Guards: Commander Fox (Borinswordbane), many others remain
104th Battalion: Led By General Plo-Koon (TheWitherCraftHD) Wolffe: (GamerAced)
327th Star Corps: Led by General Aayla Secura (don't know) Commander Bly (BobbyMech)
91st Reconnaissance Corps: Led by Jedi Master Windu (don't know) Commander Neyo (MD_K47)
Blue Squadron: Led by Ashoka Tano and Axe (both I don't know)
Bravo Squad: Led By ARC trooper Commander Colt (don't know)
Clone Flame troopers: Led by Jedi General Ki-Adi-Mundi (don't know) and Commander Jet (don't know)
Domino Squad: Hevy, Droidbait, Echo, Cutup, Fives
442nd Siege Battalion: Jedi Master Ferroda (Don't know) This Battalion doesn't appear to have a Clone Commander as it this unit was made during Episode 3 so they only have Phase 2 clone trooper armor.