It does suck to do a complete re-install. that is certainly one option. However, most of the files in /usr/bin ARE root:root. These are the only ones which aren't:
-rwsr-sr-x 1 daemon daemon 51464 Oct 21 2013 at
-rwxr-sr-x 1 root shadow 54968 Feb 17 02:42 chage
-rwxr-sr-x 1 root crontab 35984 Feb 9 2013 crontab
-rwsr-xr-x 1 root lpadmin 14336 Apr 10 19:40 lppasswd
-rwxr-sr-x 3 root mail 14592 Dec 3 2012 mail-lock
-rwxr-sr-x 3 root mail 14592 Dec 3 2012 mail-touchlock
-rwxr-sr-x 3 root mail 14592 Dec 3 2012 mail-unlock
-rwxr-sr-x 1 root mlocate 39520 Jun 20 2013 mlocate
-rwxr-sr-x 1 root ssh 284784 May 12 17:04 ssh-agent
-rwxr-sr-x 1 root tty 19024 Apr 16 17:07 wall
for a standard install.
In /usr/sbin it's:
-rwsr-xr-- 1 root dip 343168 Jan 22 2013 pppd
-rwsr-sr-x 1 libuuid libuuid 18904 Apr 16 17:07 uuidd
in /usr/lib/
drwxr-xr-x 2 root utempter 4096 May 7 23:46 utempter
in /usr/local/share
drwxrwsr-x 2 root staff 4096 Aug 20 2013 ca-certificates
drwxrwsr-x 2 root staff 4096 Aug 20 2013 fonts
drwxrwsr-x 7 root staff 4096 May 8 17:11 sgml
drwxrwsr-x 6 root staff 4096 May 8 17:11 xml
and in /usr/local/lib any python directories, e.g:
drwxrwsr-x 4 root staff 4096 May 8 18:44 python2.7
cd /usr
andchown -R root:root .