The flaw affecting SSL certificates in Debian and Ubuntu systems has been fixed.  You should make sure your system is up to date via apt and check to see if your keys are vulnerable.  To check if your keys are vulnerable run

sudo ssh-vulnkey -a

This checks the validity of all the keys in standard locations.

ssh-vulnkey /path/to/key

With this you can specify any keys you've put in odd places.  If you don't know if you've got keys in odd places, you don't.  If you get a message from this command saying COMPROMISED then you know you've got a vulnerable key that is easily hacked.  That means that your SSH and hosted SSL connections are easily hackable.  If you do have compromised keys, all you need to do is run

ssh-keygen

This will regenerate your keys with updated security mechanisms that aren't vulnerable.  Remember that if you try to login to that machine via SSH or SSL from another machine that's already logged into it, you'll have to update the keys.  For SSH, all you have to do is edit your known_hosts file, just delete the entry for that machine and you'll get the new key when you login now.  For more information, hit up the Ubuntu USN page.