Doxygen 1.6.1 will generate documentation, call graphs, etc. for Fortran source code in free-format (F90) format. You are out of luck for auto-documenting fixed-format (F77) code with doxygen.
All is not lost, however. The conversion from fixed to free format is straightforward and can be automated to a great degree - change comment characters to '!', change continuation characters to '&', and append '&' to lines to be continued. In fact, if the appended continuation character is placed in column 73, it should be ignored by standard F77 compilers (which still only recognize code in columns 1 through 72) but will be recognized by F9x/F2003/F2008 compilers. This allows the same code to be recognized as both in fixed and free format, which lets you gracefully migrate from one format to the other.
Conveniently, there are about a thousand small programs that will do this format adjustment to some degree or another. Realistically, if you're going to be maintaining the code, you might as well move it away from the 1928 spec for Hollerith (IBM) punched cards. :)