Input latency, flexibility of native resolution (they don't really have one). It's been awhile since I've looked at them side by side, but I think they're still better on black levels. I suspect color reproduction has caught up though.

It's not surprising they fell out of favor though. Once the ghosting stopped being absolutely horrendous the LCD is just superior for office work. Uses less power, saves tons of desk space (and due to less weight, doesn't need a strong desk) and no flickering means a cheapo LCD is probably easier on the eyes than a cheapo CRT.

I bet the CRT wwould still be used more often if the supply chain to make them didn't fall apart when the demand disappeared.