Houdini 3 is still the best engine.

Professional tests:  Houdini 3 vs Stockfish-dev

EnginesWar rating list

Code:

    Program                          Elo     +   -  Games   Score   Av.Op.  Draws

    Houdini 3 Pro x64              : 3291    7   7  5320    63.8 %   3192   40.3 %
    Stockfish 28-10-2013 64bit     : 3266   12  12  1500    54.6 %   3234   50.9 %
The LightSpeed ratinglist

Code:

   Name                    Elo     +    - games score oppo. draws

   Houdini 3 x64           3150    2    3 54000   67%  3030   41% (€)(best overall)
   Stockfish 131111 x64s   3122    5    5 10000   58%  3065   46% (best mp-free+open)
CEGT - rating lists November 17th 2013

Code:

   Houdini 3.0 x64          3072
   Stockfish 281013 x64     3047