I'm trying to optimize my MySQL config for a verrry small VPS. The VPS is also running NGINX/PHP-FPM and Magento; all with a limit of 250MB of RAM.

This is an output of MySQL Tuner...

-------- General Statistics --------------------------------------------------
[--] Skipped version check for MySQLTuner script
[OK] Currently running supported MySQL version 5.1.41-3ubuntu12.8
[OK] Operating on 64-bit architecture

-------- Storage Engine Statistics -------------------------------------------
[--] Status: -Archive -BDB -Federated +InnoDB -ISAM -NDBCluster 
[--] Data in MyISAM tables: 1M (Tables: 14)
[--] Data in InnoDB tables: 29M (Tables: 301)
[--] Data in MEMORY tables: 1M (Tables: 17)
[!!] Total fragmented tables: 301

-------- Security Recommendations  -------------------------------------------
[OK] All database users have passwords assigned

-------- Performance Metrics -------------------------------------------------
[--] Up for: 2d 11h 14m 58s (1M q [8.038 qps], 33K conn, TX: 2B, RX: 618M)
[--] Reads / Writes: 83% / 17%
[--] Total buffers: 122.0M global + 8.6M per thread (100 max threads)
[!!] Maximum possible memory usage: 978.2M (404% of installed RAM)
[OK] Slow queries: 0% (37/1M)
[OK] Highest usage of available connections: 6% (6/100)
[OK] Key buffer size / total MyISAM indexes: 32.0M/282.0K
[OK] Key buffer hit rate: 99.7% (358K cached / 1K reads)
[OK] Query cache efficiency: 83.4% (1M cached / 1M selects)
[!!] Query cache prunes per day: 48301
[OK] Sorts requiring temporary tables: 0% (0 temp sorts / 144K sorts)
[OK] Temporary tables created on disk: 13% (27K on disk / 203K total)
[OK] Thread cache hit rate: 99% (6 created / 33K connections)
[!!] Table cache hit rate: 0% (32 open / 51K opened)
[OK] Open file limit used: 1% (20/1K)
[OK] Table locks acquired immediately: 99% (1M immediate / 1M locks)
[!!] InnoDB data size / buffer pool: 29.2M/8.0M

-------- Recommendations -----------------------------------------------------
General recommendations:
    Run OPTIMIZE TABLE to defragment tables for better performance
    Reduce your overall MySQL memory footprint for system stability
    Enable the slow query log to troubleshoot bad queries
    Increase table_cache gradually to avoid file descriptor limits
Variables to adjust:
  *** MySQL's maximum memory usage is dangerously high ***
  *** Add RAM before increasing MySQL buffer variables ***
    query_cache_size (> 64M)
    table_cache (> 32)
    innodb_buffer_pool_size (>= 29M)

and this is the config.

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port  = 3306
socket  = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket  = /var/run/mysqld/mysqld.sock
nice  = 0

[mysqld]
#
# * Basic Settings
#

#
# * IMPORTANT
#   If you make changes to these settings and your system uses apparmor, you may
#   also need to also adjust /etc/apparmor.d/usr.sbin.mysqld.
#

user  = mysql
socket  = /var/run/mysqld/mysqld.sock
port  = 3306
basedir  = /usr
datadir  = /var/lib/mysql
tmpdir  = /tmp
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address  = 127.0.0.1
#
# * Fine Tuning
#
key_buffer  = 32M
max_allowed_packet = 16M
thread_stack  = 192K
thread_cache_size       = 8

sort_buffer_size = 4M
read_buffer_size = 4M
myisam_sort_buffer_size = 16M

# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
max_connections        = 100
table_cache            = 32
tmp_table_size = 128M
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
#query_cache_limit = 1M
query_cache_type = 1
query_cache_size = 64M

#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1

log_error                = /var/log/mysql/error.log

# Here you can see queries with especially long duration
#log_slow_queries = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id  = 1
#log_bin   = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size         = 100M
#binlog_do_db  = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer  = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

The site contains 1 wordpress site,so lots of MYISAM but mostly static content as its not changing all that often (A wordpress cache plugin deals with this). And the Magento Site which consists of a lot of InnoDB tables, some MyISAM and some INMEMORY.

The "read" side seems to be running pretty well with a mass of optimizations I've used on Magento, the NGINX setup and PHP-FPM + XCACHE.

I'd love to have a kick in the right direction with the MySQL config so I'm not blindly altering it based on the MySQLTuner without understanding what I'm changing.

Thanks