Bluenose

I'm not sure I'd really count a FUDGE and Fate as d6 systems, you can a use regular d6 with them in a pinch but they're designed to be used with custom dice. I've never used anything but normal d6 for Fate, and I don't think I've ever seen the custom variety in use. It's pretty trivial for 1/2 to be -1, 3/4 to be 0, and 5/6 to be +1. I don't think anyone has mentioned it yet, but good old Tunnels & Trolls has never used anything but d6 - sometimes great bucketloads of them, but still d6.