This is the sample Manifest.xml file for deploying a Application Page (layouts page) through the solution file. It is assumed that you know how to create a WSP file.

<Solution SolutionId="540C3653-5A01-4a00-A0FA-2D2203BB3080" xmlns="http://schemas.microsoft.com/sharepoint/">
  <FeatureManifests>
    <FeatureManifest Location="FeatureName\Feature.xml"/>
  </FeatureManifests>
  <Assemblies>
    <Assembly DeploymentTarget ="GlobalAssemblyCache" Location ="Sample.AssemblyName.dll">
      <SafeControls>
        <SafeControl Assembly="AssemblyName, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b51c7c45d52dacb6" Namespace="NameSpace" TypeName="*" Safe ="True"/>
      </SafeControls>
    </Assembly>
  </Assemblies>
  <TemplateFiles>
    <TemplateFile Location ="LAYOUTS\Sample.aspx"/>
  </TemplateFiles>
</Solution>

 The above example is for a application page with code behind. <SafeControls> entry registers the dll as safe control and puts the dll in GAC. <TemplateFiles> entry puts the aspx page in the Layouts directory. Sameway you can target the others folders in the Template directory.

Satheesh Palaniswamy