Вот рабочий конфиг, попробуйте поэксперементировать в эту сторону. Только если у вас не отключено inno-db, сами скорректируйте соответствующую секцию.
Код:
[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
tmpdir = /storage/mysql-tmp
# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
old_passwords=1
# modified parameters
max_connections=1000
table_cache=2048
sort_buffer_size=8M
join_buffer_size=8M
thread_cache_size=40
thread_concurrency=2
query_cache_size = 64M
query_cache_limit = 2M
query_cache_type = 1
memlock
tmp_table_size = 64M
key_buffer_size = 200M
wait_timeout = 28800
# log slow queries
log-slow-queries=/var/log/slowquery.log
# myisam
read_buffer_size = 2M
read_rnd_buffer_size = 16M
bulk_insert_buffer_size = 64M
myisam_sort_buffer_size = 256M
myisam_max_sort_file_size = 10G
myisam_max_extra_sort_file_size = 10G
myisam_repair_threads = 1
myisam_recover
myisam_data_pointer_size = 6
# bdb
skip-bdb
# innodb
skip-innodb
#innodb_data_home_dir =
#innodb_data_file_path = /storage/mysql/ibdata1:10M:autoextend:max:100G
#innodb_additional_mem_pool_size = 16M
#innodb_buffer_pool_size = 512M
#innodb_thread_concurrency = 2
#innodb_flush_log_at_trx_commit = 2
#innodb_log_group_home_dir = /storage/mysql/
#innodb_log_buffer_size = 8M
#innodb_log_file_size = 128M
#innodb_log_files_in_group = 2
#innodb_max_dirty_pages_pct = 90
#innodb_lock_wait_timeout = 120
# misc
default-character-set=cp1251
default-collation=cp1251_general_ci
[mysql.server]
user=mysql
basedir=/var/lib
[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid
open-files-limit=32000
[client]
default-character-set=cp1251