Banner of Command only increases:
* Yorick's Ghouls and Revenant
* Mordekaiser's Clone
* Annie's Tibbers
* Heimerdinger's Turrets
* Elise's Spiderlings
* Malzahar's Voidlings
It may affect Shaco's Hallucinate, but I don't know.
It may also affect Wukong's Decoy and LeBlanc's Mirror Image, but I'm fairly certain Banner of Command only affects auto-attack damage (of which these deal none).
Zyra's Plants, Shaco's Boxes, Maokai's Saplings, etc, are classified as traps/wards. Banner of Command only affects minions.