Reference links:
5.2.1. mysqld Command Options:
http://dev.mysql.com/doc/refman/4.1/en/server-options.html

5.2.2. Server System Variables:
http://dev.mysql.com/doc/refman/4.1/en/server-system-variables.html

5.2.4. Server Status Variables:
http://dev.mysql.com/doc/refman/4.1/en/server-status-variables.html

5.13.3. Query Cache Configuration:
http://dev.mysql.com/doc/refman/4.1/en/query-cache-configuration.html

7.5.2. Tuning Server Parameters:
http://dev.mysql.com/doc/refman/4.1/en/server-parameters.html

7.5.4. How MySQL Uses Memory:
http://dev.mysql.com/doc/refman/4.1/en/memory-use.html

High Performance MySQL: Chapter 6: Server Performance Tuning
http://dev.mysql.com/books/hpmysql-excerpts/ch06.html

MySQL Administrator Best Practices
http://dev.mysql.com/tech-resources/articles/mysql-administrator-best-practices.html

Specialized links:
A.2.9. Packet too large:
http://dev.mysql.com/doc/refman/4.1/en/packet-too-large.html

ToDo:
Some less common values to research: delayed_queue_size