I think Circos may still be the most powerful option for circular plots (but keen to hear about alternatives, too).

There's the RCircos package in bioconductor if you prefer that way of providing parameters

You might find hive plots an interesting alternative for some applications. Tools to create them include the jhive java implementation and others listed on the hiveplots.net site under "Hive plot code and applications".

Hi! I'm from UGENE team. We have a simple Circular View, but it produces nice images, so I thought, you might like to try it.

Note that we're going to improve Circular View in the program future versions. Any feedback is welcome.

From what I understand, Circos still produces the best quality figures for publication. ggbio is an alternative built on Bioconductor GRanges objects and ggplot.

Here is an interactive version of circos designed for protein sequence data. It can be simultaneously used for live presentations and/or publication quality figures:

http://i-pv.org/