Ford GT 40 Mk. IV. Kicked so much butt at Le Mans that they lowered the displacement limit to 5 litres to ban it.
Porsche 917, twice. First they banned it at Le Mans with a 3 litre displacment limit. Then the SCCA banned the 917/30 with a fuel consumption rule.
Somebody already mentioned the Chaparral 2J. Crybabies had it banned before it even won a race. Scary thing is that it was nowhere near optimized. It was based on a test rig from GM R&D. If Jim Hall had been able to put that concept into one of his composite monocoque chassis, it would have been amazing.
Before that, they had banned his 2E/2G with its driver controlled wing/airbrake.
I realize there are safety and cost considerations but all the rulemaking of the last 30 years has really taken the technical interest out of racing. Other than sponsor logos the cars are almost identical now.
I'd love to see a true free formula again. Unlimited boost, toluene/heptane fuel, giant slick tires, ground effects tunnels, downforce fans, movable aerodynamic devices for downforce/braking/stability, AWD with full active diffs, full active suspension, full fly by wire system for steering/braking/shifting/engine, and probably a bunch of stuff that would be invented through competition.