What is "super" in superphosphate?
The term superphosphate is really old, even well before the concept of atoms was proposed by Dalton. Therefore it is difficult to rationalize the choice of this terminology.

In the unabridged version of the Oxford English Dictionary, you can see the earliest usage dates back to 1798 


  Chemistry. A phosphate containing an excess of phosphoric acid; an
  acid phosphate. Now disused except in superphosphate of lime, calcium
  superphosphate: cf. sense 2.
  
  1798   Philos. Trans. (Royal Soc.) 88 17   It was..Scheele who discovered, that the urine of healthy persons contains superphosphate,
  or acidulous phosphate, of lime.


Further information from the OED on the usage of "super" in chemical names confirms its use since antiquity. See antique examples


  (b) Denoting the highest proportion of a component, esp. owing to a
  high oxidation state. Now chiefly archaic or hist., except in
  superoxide n.   and in the names of certain substances used in
  industry and commerce, as superphosphate n., supersulphate n. Cf. sub-
  prefix 4b(b).  (i) Categories » [1788   J. St. John tr. L. B. Guyton de Morveau
  et al. Method Chym. Nomencl. 107   New names... Acetite of lead.
  Ancient names... Sugar of lead, Super-acetated lead.] 1811   Jrnl.
  Nat. Philos. June 78   The aqua lithargyri acetati is a saturated
  solution of the proper acetate of lead,..it is an essentially
  different salt from the super-acetate of lead. 1913   Brit. Med. Jrnl.
  4 Oct. 875/1   Dr. Latham..used the superacetate of lead in
  consumption. 1979   A. J. Youngson Sci. Revol. Victorian Med. i. 18
  Acetate or superacetate of lead combined with opium was prescribed for
  haemorrhage of the lungs.