Gemstone information is available for the following counties. Information comes from Gemstones of Idaho written by Alice Allebaugh. 
Reference: Idaho Lands website
(I’m reposting here because data has a way of disppearring off the internet.)

  • ADAMS – Rubies and pink garnets are found at Rock Flat near New Meadows. Several diamonds have been found in this same area. Sapphires and corundum crystals that sometimes show asterism also have been found in the Rock Flat area.
  • BLAINE – Amethyst is found near Hailey; copper, silver, lead and zinc minerals are abundant.
  • BOUNDARY – Opal and opalized wood.
  • CUSTER – Clear quartz, amethyst and citrine are found. Large geodes are common. Banded, red and yellow agate is scattered over the area. A forest of petrified wood is near Challis. Near the East Fork of the Salmon River is an excellent collecting locality where a variety of cryptocrystalline quartz is found in blood red sandstone. Near Challis a rare zeolite is found in greater abundance and better specimens than in any other known locality. Copper, silver, lead and zinc minerals are abundant.
  • GEM – Fire opal is found in the lava beds of Squaw Butte near Emmett. The opals are salmon pink or cherry red in color and display great brilliance. Most are very small, but some have been large enough to cut into fine stones. Near the opal deposits agates of light blue color abound. Willow Creek has deposits of agatized and opalized wood of high quality as well as massive opal that ranges in color from deep red to salmon pink to white and pale blue.
  • GOODING – Internationally famous “horse” fossil beds near Hagerman; opal and opalized wood.
  • IDAHO – Nationally famous flora beds near Whitebird.
  • LATAH – Common and fire opals have been found in the vesicular basalts. The internationally famous garnet diggings on Emerald Creek afford the collector an opportunity to find gem and star garnets in remarkably large sizes and quantities. Fossil plant remains can be found in many localities in the siltstone of the interbeds between basalt layers.
  • LEMHI – Copper, silver, lead and zinc minerals are abundant
  • LINCOLN – Opal and opalized wood.
  • OWYHEE – Areas that yield red, yellow, green and mossy jasper of unexcelled quality. The area is nation-ally known for its pink and white plume agate and for its opal, both common and fire, which occurs in vesicles in the volcanic rocks. Banded, scenic, dendritic and sagenitic agates, as well as polka dot, smoky and moss agates are also found. Succor Creek on the western edge of the county yields red and green agates in a rich two-tone combination and a round shaped nodule, which is called “thunder egg.” These are often found to be geodes with the center filled with fluids. In some the hollow center is lined with quartz crystals.
  • SHOSHONE – Copper, silver, lead and zinc minerals are abundant
  • WASHINGTON – Agates of many colors abound. The most highly prized agates are those that show an iridescence when cut into thin slabs. Petrified wood from Mann Creek northwest of Weiser is particularly beautiful. The grain of the wood is very prominent and the color is yellow, resembling natural oak. In the Beacon area west of Weiser the famous “Beacon Hill” nodules abound. These nodules are particularly beautiful because of the scenic or dendritic patterns. In some the interior is hollow and crystal lined.