I found this thread searching for "high CPU MySQL" and discovered that all the threads about this had to do with FreeBSD. We were having exactly the same problem, and had optimized our tables, dropped our full-text indexes, researched all our queries and everything else, and even with no slow queries, and few processes running, we were at 98% CPU usage.
Eventually I found two key links, and the solution:
http://dev.mysql.com/doc/mysql/en/freebsd.htmland
http://jeremy.zawodny.com/blog/archives/000697.htmlThe solution: update FreeBSD to Release 5, or re-compile MySQL with WITH_LINUXTHREADS=yes
This appears to have solved the problem for us.
Tac