BI Publisher is for creating your reports, proposals, correspondance, letters in pdf/word etc. Usually against the live application it can also be used alongside OBI. (think XMLP or Actuate/Siebel Reports replacement but it can be much more). License included in Siebel.
BI Apps is the parts of a full on OBIEE implentation serving Siebel, think ETLs, Data warehouse design etc (think Siebel Analytics). If you want to do segmentation, selection of candidates full on Marketing Analytics solution accept no substitutes. Not cheap.