To all of you, yes it works now :D:D:D:D.. It was probably noise from the breadboard. After two hours of trying to fit the break out (made wrong measurements) board to my newly soldered board it's finally working.
Here is some pictures as proof =P:
Board soldered (Front): https://dl.dropbox.com/u/74389175/BaselM3Proto/IMAG0457.jpg
Board soldered (Back): https://dl.dropbox.com/u/74389175/BaselM3Proto/IMAG0458.jpg
Breakout board attached to the board (Front): https://dl.dropbox.com/u/74389175/BaselM3Proto/IMAG0461.jpg
When you attach the USB the first time, you need the drivers delivered with SAM-BA. After installing the drivers you should get the following: https://dl.dropbox.com/u/74389175/BaselM3Proto/sam_ba_com.png
Then open Arduino IDE and upload the blink sketch. The board will restart as Arduino Due (you'll need to install the arduino due drivers that comes with the arduino IDE). After install you should get the following: https://dl.dropbox.com/u/74389175/BaselM3Proto/arduino_blink.png.
If you've got any questions hit me! =P
And by the way I've changed a small thing in the schematic so here is the updated version:
Schematic: https://dl.dropbox.com/u/74389175/BaselM3Proto/BaselsM3ProtoV1.0.sch
Board: https://dl.dropbox.com/u/74389175/BaselM3Proto/BaselsM3ProtoV1.0.brd