I'm running 13.10 x_64, and I ditched Unity in favour of Cinnamon. Now I click the "Open Containing Folder" icon beside a download in Firefox, instead of opening Nemo, it opens the Disk Usage Analyzer, and I don't know how to fix this.
For the record, suggesting I go back to Unity is neither a solution nor an answer.
After some extensive digging on Google, I discovered that, as root I can edit /usr/share/applications/defaults.list and /usr/share/applications/mimeinfo.cache and change all references to nautilus in both those files to nemo instead and the change takes effect as soon as I save. Since I am no longer using Unity, and don't even have Nautilus installed, this solution is both safe and effective.