History: I had problems with mime associations under Firefox. Firefox opened downloaded files with wrong programs. I deleted ~/.local/share/applications/mimeapps.list and now it works.
Now I noticed that the problem is transferred to Calibre and Chromium. For example, cbr files are opened with file-roller instead of evince, and directories are opened with Firefox!
Mime associations with the file browser (PCManFM) worked before and works now without problems. I'm under Lubuntu 13.10.