We were using flot when I started. As soon as I found out about protovis I redid all our charts (and boy was everyone happy with that improvement). Shortly after that, d3 came out, in which case I ported all the protovis charts to d3. NVD3 is my second go at a collection of charts for d3.js... it was re-done from the ground up, and hopefully is much more true to d3's style than my previous attempt.