I can add a few comments to this interesting thread:
General freight: There were track-side warehouses (two at Sumpter, one at Tipton, and two at Prairie until 1915, when one burned down) that received various kinds of freight throughout the year. Shipments included such things as tools, hardware, stoves, dry goods, grain, flour, and hay. After 1922 there was a Standard Oil distributor in Prairie who received bulk oil shipments in the railroad's two tank cars. Milk and cream were shipped daily to Baker from several points along the line. Station agents at all the depots handled l.c.l freight, and occasional carload shippers or receivers could arrange to have cars spotted at a house (or team) track for a few days.
Ore: During the gold-mining years, in addition to shipments from the big mines, prospectors would bring their ore in wagons to Sumpter, Tipton, or Prairie (and maybe other locations as well) to be shoveled into boxcars; the ore was placed over the truck bolsters until the car's rated weight capacity was reached. Also a huge amount of chromate ore was shipped from Prairie during World War I.
Stock shipments: There were livestock pens at Prairie, Austin, and McEwen, and for a while there was a brush corral at Tipton. A report of freight traffic for September 1921 shows that 52 cars of cattle and 13 cars of sheep were shipped from Prairie to Baker during the month. I believe that more cattle than sheep were shipped during the early years, then the mix gradually changed toward sheep. The SV denied sheep growers' requests to double-deck their livestock cars. In later years, livestock shippers in the John Day country (Prairie and Austin) found it more convenient to drive or truck their market herds/flocks to Seneca, about 30 south and west miles from Prairie, where they were shipped out to the Union Pacific main line by the standard gauge Oregon & Northwestern Railroad Company.
Wool: The sixth annual report of the Railroad Commission of Oregon, dated 15 Dec 1912, shows annual shipments by the SV of 1406 tons livestock and 344 tons wool. This was the last such report that gave any breakdown of SV freight tonnages.