For the ignored hosts issue, try installing dconf-tools using the software centre or
Then run dconf-editor
sudo apt-get install dconf-tools
Expand System and select proxy, there should be an option for ignore-hosts. Read the description and add your exceptions comma separated in single quotes. This should work for all your desktop apps.
The reason I was searching on proxy issues is to do with updates though. I've set up proxy configuration for apt by creating a file /etc/apt/apt.conf.d/02proxy with the entry
As just setting it the GUI way through system settings doesn't appear to work any more. But, even then, when something like flash gets updated it runs /usr/lib/update-notifier/package-data-downloader without any proxy settings! The only workaround I've found so far is to open a root terminal
Set the proxy settings
and then run package-data-downloader from the root terminal
Anybody know how I can get root to recognise the proxy automagically?