The following information is from my eBook on Type One Liberty Head Double Eagles at http://doubleeaglebook.com/
Before the discovery of the S.S. Brother Jonathan and S.S. Republic shipwrecks, the 1863-S was one of the rarest Civil War era double eagles from the San Francisco mint. Today it is relatively easy to locate in all circulated grades. It can be located in the lowest Uncirculated grades with just a bit of effort but it remains rare in Mint State-62 and very rare above this.
STRIKE: Most 1863-S double eagles show a soft strike as described earlier for the 1861-S and 1862-S issues. This includes a lack of definition on the curls around the face and below the ear, soft radial lines in the stars, and considerable weakness at the top of the head and on the bow. A small number show stronger strikes. These have better detail on the hair, partial radial lines, and an overall appearance which is not as soft and “sunken” as on the typical 1863-S. The majority of the Bro Jo coins are weakly struck while the Republic coins may show more detail. The better struck 1863-S double eagles carry no price premium but these are not often seen.
SURFACES: Prior to the discovery of the S.S. Brother Jonathan, it was extremely hard to find an 1863-S double eagle which was not covered with deep, detracting abrasions on the obverse and reverse. A number of non-shipwreck coins also show scratches or are hairlined from having been cleaned. A number of the Bro Jo coins were far choicer than what was known before this wreck was uncovered. These coins sometimes show grainy surfaces but not enough to keep them from being graded by both PCGS and NGC.
LUSTER: 1863-S double eagles which are not from a shipwreck tend to have subdued, slightly grainy luster. Higher grade pieces from both shipwrecks have better luster and it is frostier in texture.
COLORATION: The natural coloration for a non-shipwreck 1863-S is medium to deep reddish-gold. Some of the shipwreck coins show color variations, such as medium yellow-gold or light rose. Before these two wrecks, it was extremely hard to find an example with nice color. Today, it is easier.
EYE APPEAL: Before the discovery of the S.S. Brother Jonathan, this date was not often seen with good overall eye appeal. Today, examples with good eye appeal are easier to locate and the collector should be able to find a CAC-quality 1863-S with little or no problem.
INTERESTING VARIETIES: There were two major varieties known:
Medium S. The more common of the two has the same mintmark as seen on the 1862-S double eagle.
Small S. The scarcer of the two has the small mintmark as seen on the 1863 double eagle.
PROOFS: There were no Proofs struck.
HOARDS: There were a total of 173 found in the S.S. Republic treasure which includes 47 graded Uncirculated by NGC. There were 116 in the S.S. Brother Jonathan treasure which ranged in grade from Extremely Fine-40 to Mint State-63. Two dozen or so Uncirculated coins were found in the source, as well as another five dozen graded About Uncirculated-55 to About Uncirculated-58 by PCGS (many of these are known in higher grade holders).
BUYING TIPS: This is a date for which most of the higher grade examples are from a shipwreck. For this reason, I would suggest holding out for an 1863-S in the original holder of issue. These bring strong premiums and they are in strong demand.
AUCTION RECORD: The auction record for this date is $43,125 which was set by Heritage 2012 FUN: 5041. This coin was graded MS64 by NGC.
FINEST KNOWN: The finest known for this date is likely the PCGS MS64 owned by Bill Crawford. I have not seen the other PCGS MS64 and do not know how it compares to the Crawford coin.The finest known is a single MS64 graded by PCGS. This coin is owned by William Crawford.
TOTAL KNOWN: 1750-2500+
Very Fine: 400-600
Extremely Fine: 600-800
About Uncirculated: 675-900
POPULATION FIGURES: As of the beginning of 2015, PCGS had graded five in MS60, 25 in MS61, 14 in MS62, six in MS63, and two in MS64 for a total of 52 in Uncirculated. NGC had graded 17 in MS60, 61 in MS61, 28 in MS62, 17 in MS63, and two in MS64 for a total of 125 in Uncirculated. This figure includes 58 Uncirculated coins from the S.S. Brother Jonathan and S.S. Republic shipwrecks. These figures are severely inflated by resubmissions, especially in MS61 and in MS62. CAC has approved three MS61 examples and four in MS62.
PERFORMANCE SINCE 2002: In the current market, a non-Brother Jonathan example of this date in choice About Uncirculated (equivalent to an AU55) is worth $4,500-5,500. In 2002, the same coin would have sold for $1,750-2,250. In the current market, a nice Uncirculated in Uncirculated (equivalent to an MS62) would sell for $17,000-22,000. The same coin in 2002 would have sold for $13,000-15,000. It is important to note that this MS62 might not be attributed to the S.S. Brother Jonathan today as many have been cracked out of their original holders. In 2002, this was not the case. This date has performed well in AU55 but it has been a poor performer in MS62. This leads me to believe that this date was well overpriced in 2002 and it has taken the market close to a decade to catch up to and finally surpass these older levels.
COMMENTS: Many non-specialists assume that since this date has been “Bro Jo’ed” it is no longer scarce in higher grades. This is not the case as many of the shipwreck examples located were in About Uncirculated grades. It is unfortunate that a number of the nicer shipwreck 1863-S double eagles have been removed from their original holders, upgraded and are now confusing to collectors as to their status. As a rule, examples with original surfaces tend to be a bit more vibrant but tend to show more marks. The shipwreck coins have a more subdued appearance and tend to show few marks of note.
David Akers (1975/88):
The 1863-S is a moderately scarce date in all grades with most of the available specimens grading only VF or EF. In AU, this date is very scarce and in average uncirculated condition it is quite rare. Choice and gem quality examples do exist but they are definitely rare. However, among Type I Double Eagles from the San Francisco Mint, this is one of the most often encountered dates in original uncirculated condition.