A typical configuration file for MySQL 5.1 would be something like this (link downloads my.cnf from our FogBugz instance). These numbers are geared toward a server only running FogBugz and MySQL using 2GB of RAM. It is recommended to scale the numbers linearly if you have more RAM than that UNLESS you have a large amount (more than 32GB of RAM). If you have that much RAM, consult your DBA about correct values.
This file is made for use with 5.1. Please keep in mind that this will also work for MySQL 5.5, but NOT for MySQL 5.0 due to variable renaming. Most of the variables have similar options in MySQL 5.0. You can find the list of them for MySQL 5.1 here and the MySQL 5.0 options here.
Finally, there are several path-related variables in the file. They were initially written for Linux, which has a fair amount of variety in where you might store your sockets and PIDs. And Windows is an entirely different beast. Make sure you go through and change those variables to be relevant to your installation before using this. You can always compare those paths to the paths in the default my.cnf/my.ini file to know what they should be.
If you have any trouble, please contact us.