Mail/limewire/skype Problems - Network fine!

My mail was working fine the other day, but suddenly it won't connect to any of my email accounts (gmail, university email account, etc). I tried installing Thunderbird and read my messages through that but it still won't work.
Additionally, skype stopped working too. It said I could connect but it would show that no users were online, when they were infact online. However, I reinstalled it and it solved the problem. But mail still won't work...
I looked at my firewall settings and they seemed ok.
The internet/network connections are working completely fine. I can browse normally with Safari. The only things that have changed are Mail and Limewire. Limewire no longer connects properly and mail can't seem to connect to any of my accounts. No preferences have changed to my knowledge. I even tried dragging the preferences folder to the desktop and let the preferences go to the default, however, Mail still did not work
Any ideas?

I tried all of the above.
At first when I did the Disk Utility functions, I got an error that my Disk could not be repaired, however, once I booted into safe mode, it said it could be verified and found no errors.
Mail/Limewire still dont work!

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