Apps, specific tasks or system preference panes won't open in mountain lion

I am having a weird case. It started with a POP mailbox that had issue to display the emails. Whatever I tried the mailbox couldn't be restored/rebuilt/imported - the mail app was hanging and had to force quit it. Preferences files removed, I also remove the whole mail folder inside my Library and tried to setup from the beginning a gmail I have, and the behavior was strange, as it didn't auto-found the gmail settings with IMAP as usual.

Then, after clearing caches, repairing permissions, checking for volume structure (no problems found), the whole issues expanded.

Many apps now do not open e.g. Skype and App Store, iTunes... Also most of the system preferences won't load - the app hangs at "Loading Network...". While I can open the users preferences, it won't let me authenticate to unlock the preferences. - it hangs after clicking the button.

What can be wrong? I am looking for possible fixes without resorting to format and restore.