Assuming that WSS was installed in the default installation location, which for most WSS files is C:\Program Files\Common Files\Microsoft Shared\web server extensions\12 and for the virtual directories is C:\Inetpub\wwwroot\wss\VirtualDirectories\, when the solution is deployed each file described in the solution manifest elements is copied to a praticular location. Here is a list of these locations:
Assemblies
The parameter DeplymentTarget determines whether to deploy the assembly to the GAC or to a directory (WebApplication).
With the GAC option assemblies are copied to C:\WINDOWS\assembly. With the WebApplication option the files are copied to C:\Inetpub\wwwroot\wss\VirtualDirectories\80\bin.
Features: C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\FEATURES\
TemplateFiles: C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\
Application Resources: C:\Inetpub\wwwroot\wss\VirtualDirectories\{virtual app port}\resources
Global resources: C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\FEATURES\
Web Parts: C:\Inetpub\wwwroot\wss\VirtualDirectories\80\wpcatalog
Site definitions
The SiteDefinitionManifests list contains descriptions of all site definition folders. The Location attribute defines the name of the folder that contains the site definition. This folder contains the ONET.xml and other components of the site definition.
Target Folder: C:\Program Files\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\SiteTemplates