A school project of mine was porting there existing development boards to the arduino IDE.
My school uses there own development board with a atmel at90can128 mcu.
It has a onboard jtag ICE programmer based on a atmega16.
It has 1 usbport emulation 2 comports (FTDI ft2232d) one is connected to the jtag programmer, and one is connected to a uart of the at90can
And all the other stuff like power regulator leds and stuff.
Now I have made the core file for this board, but it should work with any at90can, you need maybe a different pins.
It also supports CAN bus, I've used the atmel CAN library for this http://www.atmel.com/dyn/resources/prod_documents/at90CANLIB_3_2.zip
I have modified it so it works in the arduino IDE.
Check the atmel library out how it works, with the examples.
I have included 2 sketch's with CAN support.
The CAN support works only with the at90can of course, its embedded in the mcu.
And as last to make it complete, it also has a bootloader.
Here are the core files: http://18.104.22.168/~superkoe/arduino/at90can.zip
It supports the arduino IDE 0018