In addition to the tragedy of Samuel's life being cut so tragically short, since he was born after the 1860 census was taken and died before the 1870 census, there is no way to know for sure who his parents were. The possible parents are:
David Downen and his wife Manerva Standard Downen
Henry Downen and his wife Anna Reed Downen
Samuel Downen and his wife Mary Hendrickson Downen
I picked through the census records and other information on the three families. I can't rule out Henry and Anna as possible parents, but Anna was still alive for the 1900 census and she noted she had born three children, and those three children are all known and accounted for (one with Henry and two with her second husband Daniel Shoop. So it seems likely that we can rule out Henry and Anna as the parents, if that information from the 1900 census is correct.
David and Manerva were a possibility, but less likely than Samuel and Mary. This is because of the birth dates of two of their children who bookend the birth of Samuel, Ida and James. It is believed that Ida was born in October 1860, only four months before Samuel. The records for James indicate he was born in February 1862, right around a year after Samuel.
It would be possible to contort things so that James and Samuel could be brothers, even with their births only a year apart. But if that birth date for Ida is correct, there is no way that Manerva could be Samuel's mother, it's just not possible. So that would seem to rule out David and Manerva as his parents.
This brings us to Samuel and Mary. Samuel died in 1861 and it looks like Mary remarried her second husband Andrew Wilhelm around 1865. She is known to have had at least three children with him. When she was noted in the 1900 census, she was recorded as being the mother of six children, of whom two were still alive (these would be Edith and Jesse Wilhelm, her son Thomas Wilhelm having died at the age of four or five). There is a good likelihood that one of those deceased children could have been Samuel, since there are no recorded children being born to Mary and Samuel.
There is also the thought that Samuel could have been Samuel Jr., and he could have been named after Samuel Sr. since that was his father. It does seem kind of obvious. That by itself wouldn't be proof, but after running through the other speculations that are on this page it would seem that Samuel and Mary are the most likely parents, by a longshot. So I'm going to go ahead and link them to his record as his parents.
See also Francis M. Downen, who is very likely to be a sibling of Samuel's. The research I have done on Francis also points to Samuel and Mary being his most likely parents. But it doesn't seem as strong to me as the evidence for Samuel, so I haven't linked him to them as their child.
See also Evaline Downen, another potential sibling.
The Vail Cemetery is in west central Illinois, so I am unlikely to get there any time soon to see if the proximity of the markers to each other gives some clues as to who belongs to which families. There are at least 17 Downen family members buried in this cemetery, if not more. The only family with more members there than the Downens is the Vail family (presumably the people the cemetery is named for).