In practice most powers are exercised by Ministers - even those personally exercised by the Monarch are done on advice of Ministers, or according to established conventions. The Public Administration Committee in the House of Commons produced a report on the Royal Prerogative http://www.publications.parliament.uk/pa/cm200304/cmselect/cmpubadm/422/422.pdf.
Reform of the Royal Prerogative forms a major plank of the Government's proposals for constitutional renewal. Relevant documents can be accessed at http://governance.justice.gov.uk/
In the GCHQ case (Council of Civil Service Unions v. Minister for the Civil Service [1985] AC 374) the House of Lords held that the Courts could review the use of the Royal Prerogative.