Regarding "large dots in a line".
I haven't actually driven out to check these items, but they are almost certainly modern and related to energy development. Since they are regular and laid out on a grid, I suspect that they are:
1. Uranium exploration boreholes drilled by water-well sized rigs in the 1960-70's, or
2. Shot holes for seismic exploration for natural gas within the last 10-20 years.
3. Unlikely, geochemical test borings for natural gas or sodium carbonate (trona) exploration.
4. Unlikely, rock cairns built by land surveyors to mark section corners during the early Government Land Office cadastral land surveys in the late 19th century.
This area has been extensively covered by archaeologists as required by the Bureau of Land Management prior to energy development. The nearly-rectangular areas of disturbed earth to the north and east of the tags are natural gas well locations. Given the amount of energy activity in this area for the last 30 years, it is extremely unlikely that archaeologists would miss any prehistoric traces.
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Regarding the randomly scattered little dots...
... I think you've identified prairie dog burrows. The spacing (40-60 feet) looks about right. In a well-used area, most of the burrows are probably abandoned, so the animal population isn't nearly as big as the photos imply.
Photographic artifacts like the ones you identified can visibly persist in this arid climate for quite some time because vegetation takes a long time to recover. You should still be able to see remnants of the Immigrant Trails (Oregon, Mormon, etc), to the south and east of these sites. One possible section (right location, but might have been improved at some point) is visible at 42 degrees, 35' 18.19" North, 106 degrees, 59' 24.90" West.
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Finally, regarding the black "dots close to a water area"... those are undoubtedly cattle.
If I have the occasion to drive out there later this summer, I'll look around and try to take some digital photos to post.
Dave - Casper, WY.