Site templates and site definitions are two separate customizations you can undertake. You need to make a decision based on your requirements as to which is best.
Site templates
Pro's:
- Easy to create and reuse through the SharePoint interface
- Ideal for end users
- A site template is a customization of the underlying default site definition
Con's:
- Dependency on underlying site definition means SharePoint updates could break your site templates
- Poor performance since the modifications are held in the database and are read from the DB and compiled on each request
- Limited customization options
Site definitions
Pro's:
- Made by developers and site administrators
- Independent of SharePoint default site definitions so not affected by SharePoint updates
- Limitless customization options
- Can be cached on the file system so is fast to load
Con's:
- Harder to create: involves coding XML
- Difficult to modify when deployed
Note: The site template does not store the complete definition of a site - only the differences from the underlying site definition. Move the site template from one site collection to another and you lose the underlying site definition and run into problems such as missing content types (since these are part of the site definition).
Check out Google for info on creating custom site definitions.
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