With Samuel, we are getting back to biblical names from a Hebrew origin. Samuel, meaning either "Name of God" or "God has heard," was the name of the Old Testament Judge who anointed kings Saul and later, David.
The name Samuel is slightly different from some of the more popular names on the list, in that nowadays it is rare to find a Samuel who actually goes by Samuel. For example, a Benjamin can go by Benjamin or by Ben, and his choice may define his self-identity. Samuel on the other hand, will most likely go by Sam. The end result is that a person's given name will only be his official name, not the one he will go by.
Perhaps this is the reason that, even though there have been slight shifts in popularity throughout the years, the name remains popular, but not as popular as other classic names with single-syllable nicknames.
2010 Update:
The name moved up a bit, to number 24.
