GUI for stockfish that can analyse the full game I am looking for a GUI for stockfish that can analyse the whole chess game and give me the following output: For every move in the game, it should give me a list of N (let it be 3) best moves with a score corresponding to each of these moves.

Here is a good example. As you see, after each move I can see a corresponding best replies and their score. I need this to analyse a few hundred games automatically.

P.S. just to be clear. I do not need a software to do this with few hundred games. If it can analyse one game in the way I want, I can make it analyse all games. I just wanted to show a high level picture what I am planning to do. Sorry, that it was misleading.
Yes, this is possible. But in a slightly crude way. It is possible with Arena Chess GUI 3.5. What you need to do is the following-

1) Open the pgn file in Arena GUI

2) Confiure any engine with Multi-PV enabled to your choice of top "N" moves.

3) Now open Engines > Automatic Analysis

4) In Source tab select "List of EPD/PGN Files" and Click the icon for adding all PGN files for which you need the automatic analysis.

5) Check "WhiteMoves" and "BlackMoves"

6) If the PGN file contains multiple PGNs then select the range of game numbers you want it to process

7) Select range of move numbers if needed

8) Now go to the Output tab and select "Write in protocol file"

9) Now start the analysis and after its done, you can check the protocol file. The last section for each move contains the best "n" moves calculated by the engine. Parsing this protocol file should be really easy if you want to automate it.

Note: The pgn itself can be altered to add the scores, but it does not add multiple moves at one shot.

Example output in the protocol file:

   ---------------------------------------------------------------------------
16/25   00:01      3,444,292    2,274,961   -0.04   0-0 Ne5 Nc6 Nd2 Rd8 Qb3 Bd7 0-0 Qc7 Re1 h6 Ndf3 Ne4 Nxd7 Rxd7 Ne5 Bxe5 fxe5 Qb6
16/25   00:01      3,444,292    2,274,961   -0.08   Nc6 Ne5 Bd7 Nd2 0-0 Qb3 Qc7 0-0 Rfc8 Re1 h6 Ndf3 a6 Bd3 Na5 Qc2 Nc4 Bxc4 dxc4
16/25   00:01      3,444,292    2,274,961   -0.08   Bd7 Qb3 Qc7 Ne5 Nc6 Nd2 a6 0-0 0-0 Re1 Rfc8 Bd3 h6 Ndf3 Na5 Qc2 Nc4 Bxc4 dxc4
8/16/2014 12:24:59 PM, Time for this analysis: 00:00:02, Rated time: 00:04


Of course it also has flexibility to tailor what gets dumped into the file as well.