MySQL 5.1 High Cpu usage on CentOS 6 I am running MySQL 5.1 on a CentOS 6 server with 16G ram. I got also apache on it.
MySQL is constantly using too much cpu.
top - 17:40:36 up 112 days, 12:13,  1 user,  load average: 1.24, 1.72, 1.82
Tasks: 222 total,   1 running, 221 sleeping,   0 stopped,   0 zombie
Cpu(s): 12.3%us, 11.6%sy,  0.4%ni, 72.9%id,  2.8%wa,  0.0%hi,  0.1%si,  0.0%st
Mem:  16329040k total, 12946136k used,  3382904k free,   587252k buffers
Swap:  1051832k total,  1050988k used,      844k free,  4986272k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                                                                 
25368 mysql     20   0 8854m 5.3g 5064 S 295.4 33.9  11912:37 mysqld                                                                                                                                 
 1757 apache    20   0  982m  80m  28m S  2.0  0.5   0:03.04 httpd                                                                                                                                   
 2494 apache    20   0  878m  68m  27m S  2.0  0.4   0:00.92 httpd   

my.cnf
[client]
default-character-set=utf8

[mysqld]
local-infile=0
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
symbolic-links=0
bind-address=127.0.0.1

key_buffer        = 800M
max_allowed_packet    = 32M
thread_stack        = 256K
thread_cache        = 8
thread_cache_size    = 20
thread_concurrency = 4
max_connections        = 510
table_cache            = 9000
interactive_timeout = 80
tmp_table_size = 540M
max_heap_table_size = 540M
max_connect_errors = 150
wait_timeout = 20
read_rnd_buffer_size = 1024K
connect_timeout = 10
query_cache_type = 1
query_cache_limit   = 40M
query_cache_size        = 128M
innodb_buffer_pool_size = 256M

join_buffer_size = 14M
sort_buffer_size = 14M

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

SHOW FULL PROCESSLIST; is returning me on average 2-5 queries.
Here is the output of SHOW VARIABLES; command.
We got MyISAM and InnoDB tables in this system.
Thank you for any suggestions.
EDIT 1
Here is the vmstat output.
EDIT 2
SHOW GLOBAL STATUS output is available below in the comments.
Let's see the slowest query in the system.  Quite likely, fixing it (adding an index, reformulating the SELECT, etc) is the best solution.  You mentioned SHOW FULL PROCESSLIST -- That is likely to show the naughty queries; let's see them, plus the associated SHOW CREATE TABLEs.

query_cache_size        = 128M -- too big; no more than 50M.  A big value slows down the system with pruning.

innodb_buffer_pool_size = 256M and key_buffer        = 800M -- What ENGINE are you using?  Neither of these values is likely to be 'good'.  See http://mysql.rjweb.org/doc.php/memory for further advice.  A poorly-sized cache could lead to extra I/O, which would be seen as slow queries.

table_cache            = 9000 -- Yikes!  How many tables do you have?  (Thousands of tables is an OS problem.)