For the Netduino Mini, follow this wiki page.
Download and install SAM-BA 2.12 CDC for Windows (XP, Vista, Seven editions) from this download page
(You will have to register to download but there is no costs). For best results update your windows driver (using device manager) to the drivers located in (depending on your system) Program Files\ATMEL Corporation\sam-ba_2.12\drv BEFORE using this tool. If this does not work for you, some success has been using the SAM-BA 2.9 non-CDC available here
Fully reset the Netduino by connecting +3.3V to the metal square below Digital I/O pin 0 while the Netduino is powered up.
Now (re)connect the Netduino to the PC. A driver for an emulated COM port will be installed. Start the SAM-BA tool.
If a driver for an emulated COM port is not installed on a Windows 7 x64-machine, try this wiki page
Select the serial port (COM port) the Netduino is connected to, select the right chip for your Netduino and click "Connect". The chip information for your Netduino is on the device itself. The chip will have "Atmel" stamped on it, and the chip will have an identifier like "at91sam7x512-ek." The actual value will depend on the particular Netduino you have.
Now we need to execute two scripts. First, select "Boot from Flash (GPNVM2)" and click on "Execute".
Afterwards we need to do the same with the "Enable Flash access"-script.
Now make sure we're in the "Flash"-tab. By "Send File Name" select the "TinyBooterDecompressor.bin" file and click "Send File". This file is found in the Netduino Firmware ZIP file in the latest forum thread
Then we get a message about locked regions. Click "No"
After that we can close the SAM-BA tool and test if it's actually done. To do so, reconnect the Netduino and start MFDeploy.exe.
Select USB and the Netduino, then click Ping.
Now you're ready to flash the firmware