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Doxygen now supports FORTRAN 90 using !> and !< for special comments and !> or !! for special comment continuation. For example

  !> This is documentation of the 
  !! subroutine test.
  !! @param B doc for second argument
  !! @todo Handle special case
  subroutine test(A,B,C)
    implicit none
    Type(mytype), intent(in) :: A !< doc for first arg    
    Type(other), intent(in) :: B
    Type(another), intent(out) :: C !< doc for thrid arg

The current LIBISIS doxygen documentation is at

Examples of other projects documented using this system are DOUG and TDTB+UJ