How to run a B2PLYP-D3 calculation in Gaussian 09?
Search for B2PLYP on the Moller-Plesset page:


  B2PLYPD3 requests the same but with Grimme's D3BJ dispersion [Grimme11, Goerigk11].


The correct D3 parameters will be set for you automatically.

%nprocshared=4
%mem=4gb
%chk=fohsdft3
# opt freq b2plypd3/aug-cc-pvdz scf=tight

Input file taken from fohsdft

0 1
O                  -3.46278   2.54045   0.
H                  -2.50278   2.54045   0.
H                  -3.78324   3.44539   0.


Since B2PLYP-D3 is a method, it goes where the density functional is normally specified.