Workbench tools come from five toolboxes, and each one raises Joel's tool level, which unlocks stronger weapon upgrades at workbenches. Finding all of them earns the Sharpest Tool in the Shed trophy.
Bill's Town: in the church basement, or later in a garage before the high school. Pittsburgh: in the garage of victims' belongings after the hunter ambush, or on a table by a security booth after jumping the bus. The Suburbs: in an equipment room in the sewers after the moving platform, or later between beds and a shelf in a room with a broken window. The University: behind the shiv door at the end of the science building's second-floor corridor. Bus Depot: in a FEDRA triage tent.
Missing too many toolboxes leaves you short of level 5, which means another playthrough for the trophy.