This is the ponyprog programmer, basically. You can use PonyProg, or AVRDude (I believe the programmer is called “ponyser”).
In order to communicate between your PC and the AVR, you will need an RS232 to TTL converter. Try the cp2103 breakout from SparkFun, or if you’re interested in making the circuit yourself, use a max232 or max233 solution (detailed schematics are in the application notes).
ICSP programming is dead simple. You can figure it out from the PonyProg web site and the data sheet for the AVR. basically, plug the programmer into your breakout board (make sure Pin1 is in the right spot), and the other end into the PC. Fire up ponyprog and away you go.
You should be aware that the Atmega128 ships in 103 “compatibility” mode, which (IIRC) will disable one of your UARTS. You can disable this mode from PonyProg, by unsetting the relevant fuse bit.
actually, unlike the ATmega128, the AT90CAN128 does not have “103 compatibility mode” so you don’t need to worry about it. However I think it ships with clock/8 set and you probably don’t want that fuse on.
ponyprog is painfully slow so personally I use Atmel’s real ISP device, the ATAVRISP (and now the ATAVRISP MkII which, ironically, uses a mega128 inside). It’s available from All American but they ship orders very slowly. Hopefully someone else can supply it too (digikey still doesn’t stock them). The MkII ISP uses USB and programs the AVR ridiculously fast.
if you use ponyprog I suggest that you burn a bootloader capable of downloading new application code and then use only that for programming from then on.