Its probably a bit dated now, but one of my first (& favourtite) holy wars was the Amiga Versus the Atari ST.
Of course, I had an Amiga, 'cause it kicked @ss! The only thing the Atari had going for it was a built-in midi interface. The Amiga though had more colors available AND 3 stereo channels as far as I remember. Brilliant machine!
N.B. my very first holy war was the ZX spectrum Versus commodore 64... kinda lost that one cause C64 turned out to be a bit better, still loved the old spectrum though!