Another thing to watch for with Gentoo is the way it configures the max file size to 128M:

[extract from /etc/mysql/my.cnf]
# you may wish to change this size to be more suitable for your system
# the max is there to avoid run-away growth on your machine
innodb_data_file_path = ibdata1:10M:autoextend:max:128M

If you start getting "Table 'foo' is full" errors, check your config file.

This is kind of a got ya and either isn't in the documentation or is as clear as mud. When you want to change the location of the innodb data files you have to set both the innodb_data_home_dir and innodb_data_file_path variables. So in my case, I was trying to move the data file location to /History/mysql. So I tried adding to my.cnf

innodb_data_file_path=/History/mysql/ibdata1:10M:autoextend:max:15G

Upon starting mysql, I got an error unable to open database. When I looked in syslog, the innodb_data_file_path looked like this
.//History/mysql/ibdata

I added to the my.cnf

innodb_data_home_dir=/History/mysql

and modified innodb_data_file_path to

innodb_data_file_path=ibdata:10M:autoextend:max:15G

and mysql started up using the correct file paths. Remember to change the permissions on the /History/mysql directory to chown mysql:mysql mysql. All is well and I was also able to change the log file locations as well.

From this part of the doc:
# Set key_buffer to 5 - 50% of your RAM depending on how much
# you use MyISAM tables, but keep key_buffer_size + InnoDB
# buffer pool size < 80% of your RAM
It is not really clear but 'key_buffer_size' is a MyISAM parameter so the sentence above means that the more you use MyISAM table the higher key_buffer_size should be.

It wasn't really clear to me at the beginning.