I had the same problem on Feisty (upgraded from Edgy), but for me the
solution wasn't in the .local directory, but in the .config directory.

IOError: [Errno 13] Permission denied:
'/home/frans/.config/menus/applications.menu'

so after

sudo chown -R <user>:<user> .config

Alacarte worked as advertised.

-- 
Alacarte doesn't take anything into account or crash
https://bugs.launchpad.net/bugs/66705
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