I have been using MySQL Tuner (http://mysqltuner.com) on Linux for a while and am quite comfortable with it. Now, for whichever reason, we have had to start hosting other websit
Don't know of another tool (outside the MySQL Instance Configuration Wizard you can run) like mysqltuner which will not run unfortunately. You can install Perl on Windows, but when run the .pl file you will get an error about $PATH not having mysqladmin in it. Upon reading of the manual laughing, it plain as day states there is no Windows support for 1.2.0 version of tool.
You can see if these suggestions help in the interim: http://www.mysqlperformanceblog.com/2006/09/29/what-to-tune-in-mysql-server-after-installation/
Edit: I just found this: http://www.webyog.com/webyog/monyogscreenshots MONyog, it is a paid product, though. I installed the trial and it looks very promising. It monitors your SQL server and gives you alerts and recommendations based on those alerts. Might be worth a look. I cannot vouch for too much other than it has some nice information in just a short period of time.