A holo-plan was a blueprint for an extremely powerful Gadgetron weapon. After deciding the weapon was too lethal, Gadgetron institutionalized the scientists who worked on the weapon and broke the plan into pieces, which were then scattered around Polaris. There was one piece on most planets in the Polaris Galaxy that Ratchet could explore on foot. They were usually hidden in out-of-the-way areas (such as inside an average crate) so that they could easily be overlooked by the unwitting hunter.
The holo-plans, when assembled, were used to build the RYNO IV, the superweapon in Tools of Destruction. The Smuggler offered to build the weapon for no "monetary compensation." However, he did request to keep the holo-plans (presumably to sell them, or to build the weapon for himself). Regardless, the complete holo-plan is still displayed in the Inventory after making the trade.
Holo-plans were later used in A Crack in Time to