MySQL conf file for OS X 10.8.3 with MySQL version 5.6.x. Make sure that all folders are owned by your user account, or have permissions to them.

my.cnf

# Generated by Percona Configuration Wizard (http://tools.percona.com/) version REL5-20120208
# Configuration name mysql-gazelle generated for yellow5c@gmail.com at 2012-07-26 16:25:45

[mysql]

# CLIENT #
port                           = 3306
socket                         = /usr/local/var/run/mysqld/mysqld.sock

[mysqld]

# GENERAL #
# default_storage_engine         = InnoDB
user                           = mysql
default_storage_engine         = InnoDB
socket                         = /usr/local/var/run/mysqld/mysqld.sock
pid_file                       = /usr/local/var/run/mysqld/mysqld.pid

# MyISAM #
key_buffer_size                = 32M
myisam_recover                 = FORCE,BACKUP

# SAFETY #
max_allowed_packet             = 16M
max_connect_errors             = 1000000
skip_name_resolve
innodb                         = FORCE

# DATA STORAGE #
datadir                        = /usr/local/var/mysql

# CACHES AND LIMITS #
tmp_table_size                 = 256M
max_heap_table_size            = 2048M
query_cache_type               = 0
query_cache_size               = 0
max_connections                = 500
thread_cache_size              = 50
open_files_limit               = 65535
table_definition_cache         = 4096
table_open_cache               = 4096

# INNODB #
innodb_flush_method            = O_DIRECT
innodb_log_files_in_group      = 2
innodb_log_file_size           = 512M
innodb_flush_log_at_trx_commit = 0
innodb_file_per_table          = 1
innodb_buffer_pool_size        = 1G
innodb_data_file_path          = ibdata1:10M:autoextend:max:3999M

# LOGGING #
log_queries_not_using_indexes  = 1
slow_query_log                 = 1