Hi. Basically, I wouldn't touch /usr at all - it looks fine to me and isn't likely to grow in any significant way in the forseeable future.
/var is another matter, but 45% isn't too much of a problem. That said, you should be able to issue the following to clear down some of the logs, retaining the emptied files. It would be an idea to do this on a fairly regular basis.
cat /dev/null > /var/log/lastlog
cat /dev/null > /var/log/maillog
If you're happy that you've read all of root's mail and acted on it, just opt to read the mail and delete each entry. If there are hundreds of root emails, just reset the file as above, ie
cat /dev/null > /var/mail/root
Also check for any other large mail files in /var/mail and zeroise them in this way.
Hope this helps.