I'm late to this discussion, but it's one I'd like to join. :-) Terry Thornton at The Graveyard Rabbit of the Hill Country started with Grave Marker Symbols: The Southern Cross of Honor and UCV. Judith Shubert at The Graveyard Rabbit of the Covered Bridges continued with Hood County Texas: C.S.A. Veterans & Southern Cross of Honor Symbol. [UPDATE, 1 June 2009: Judith has moved this post to the blog, Cemeteries with Texas Ties. The link has been corrected to reflect this move. You may also link to her article via her nice comment on this post.]Wikipedia states:
The Southern Cross of Honor was a military decoration meant to honor the officers, noncommissioned officers, and privates for their valor in the armed forces of the Confederate States of America during the American Civil War. It was formally approved by the Congress of the Confederate States on October 13, 1862, and was originally intended to be on par with the Union Army's Medal of Honor.In respect to gravestones, the U.S. Veterans Administration issued Confederate stones with the Southern Cross of Honor symbol engraved at the top. It is only issued by the V.A. for graves of Confederate veterans.
The design for the face of the medal consists of a cross with a Confederate battle flag surrounded with a laurel wreath, with the inscription "The Southern Cross of Honor." On the back of the medal is the motto of the Confederate States of America, "Deo Vindice" ([With] God [As Our] Vindicator), and the dates 1861 1865.
Another form for the Southern Cross of Honor is a cast iron reproduction of the medal described above. It is usually atop a medal rod and placed in the ground at the Confederate soldier's grave. This cross is often placed on Confederate graves by local chapters of Sons of Confederate Veterans. This form of the Southern Cross of Honor is sometimes referred to as the "Iron Cross of Honor" or "SCV Iron Cross."
In most of the local cemeteries I've visited, there is often no Southern Cross of Honor found on a Confederate veteran's gravestone. Many Confederate veterans have no mention of their service on their gravestones at all. Sometimes the service is recorded on the gravestone, but it is still not accompanied by a Southern Cross of Honor. In many cases, stones recording the service of the veteran were clearly added years after their death.
In slightly fewer instances, V.A. issued headstones are found. These may have the Southern Cross of Honor engraved on top, or the engraving may be of a traditional cross. In these cases, the Confederate service is recorded in varying degrees. I presume this is based on how much information is known since these stones, too, were sometimes clearly added many years after the death of the veteran.
The cast iron Southern Cross of Honor is rarely seen in my local cemeteries. I cannot give a particular reason for this. Maybe the local chapters of Sons of Confederate Veterans or United Daughters of the Confederacy do not have the funding to provide these memorials. (I have heard of both of these organizations bestowing Southern Crosses of Honor to veterans' gravesites.)
On a recent trip to Hillcrest Cemetery in Reynolds, Taylor County, Georgia, I saw many examples of the Southern Cross of Honor. Here are the ones I recorded:
Died May 19, 1910
Age 64 Yrs
[no mention of service on tombstone; iron Southern Cross added]
R. Crawford ParisDied January 1, 1909
[no mention of service on gravestone; iron Southern Cross added]
Matt H. BarrowCo K
62 Regt
GA Inf
CSA
1837 - 1929
[Southern Cross engraved on VA stone]
William Wiley RicksCo K
25 GA Inf
CSA
[Southern Cross engraved on headstone; iron Southern Cross added at foot]
Father
Emanuel Aultman
Born Jan 27, 1830
Died May 29, 1915
Asleep In Jesus
[no mention of service on tombstone; iron Southern Cross added at foot]
W. H. Christopher, M.D.Sept 25, 1818
Nov 8, 1885
[new stone with iron Southern Cross]
Thomas Jefferson MarshallCapt Co E 6 GA Vol Inf
Crawford Co Greys
Confederate States Army
Feb 21, 1834 - Jan 8, 1905
[iron Southern Cross at head; no mention of service on first gravestone; new stone with Southern Cross engraved and information added]
Henry Theodore Coleman
May 4, 1848
Apr 29, 1904
[no mention of service on gravestone; iron Southern Cross at head]
This is probably not the last you'll read on this subject on this Southern Graves blog!
Once again, the work of a fellow 
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John 14: 1-3