Most of the sites referenced here tell you to use a feature which changes the masterpage, which holds all your webpart zones, where they're located and what webparts are in those zones. After you've created a MySite masterpage which has the look and feel you want, you need to deploy the feature to switch masterpages. In addition, you need to add a feature which staples the original feature (which changes the masterpage) to any new site that is created. Inside your staple feature, you can specify which site types you want to staple the feature to.
Here is a good article which doesn't require you to write code, but does require you to create both of the features and deploy them: http://www.sharepointblog.com/2008/07/sp2007-custom-master-pages-on-subsites.html
The area where you'll want to pick out which site type the feature to change the masterpage applies to (what site type the feature is "stapled" to) is:
FeatureSiteTemplateAssociation Id="bb77f112-2cda-4e92-b0ff-820c0216a7fe"
TemplateName="STS#0"/> (this will staple it to the global template, any site created)
Here is a listing of the type of sites you can staple to: http://social.technet.microsoft.com/forums/en-US/sharepointgeneral/thread/721bec39-2d32-4bbc-9094-a021a0d06dcb
So, if you want to staple the feature to just MySites, you'd put this into your stapler feature:
FeatureSiteTemplateAssociation Id="bb77f112-2cda-4e92-b0ff-820c0216a7fe"
TemplateName="SPSMSITE#0" />
You'll notice from the example that I posted a link to above, the stapler feature references the masterpage switching feature by the Id you supply in the FeatureSiteTemplateAssociation part of you stapling feature.