I am posting the whole KB944105 because we need some more attention on the subject:

http://support.microsoft.com/kb/944105

INTRODUCTION

This article describes two methods to customize the appearance and the behavior of your site collections in Microsoft Office SharePoint Server 2007 and in Microsoft Windows SharePoint Services 3.0.

 

MORE INFORMATION

Modifying the files that are installed by SharePoint is not supported. However, there are some scenarios in which you may have to modify these files to achieve consistent branding or other customizations. When you modify these files, you must consider that they may be replaced by future updates and service packs. Additionally, there may be complications when you upgrade to later versions of the product. Keep backup copies of all customized files in case they are overwritten by an update. Product support will provide commercially reasonable support for help with modifications but will be unable to provide product changes or hotfixes that result from modifying the files that are installed by SharePoint.
To customize the appearance and the behavior of your site collections, use one of the following methods.

 

Method 1: Customize the files in the Layouts folder (recommended)

1.
Create a Layouts_Backup folder to contain a backup of the originally installed files and folders. For example, create a Layouts_Backup folder in the following location:

C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Layouts\Layouts_Backup

2.
Copy the originally installed files and folders from the Layouts folder to the Layouts_Backup folder that you created in step 1. For example, copy the originally installed files and folders from the following folder to the Layouts_Backup folder:

C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Layouts

3.
In the Layouts folder, customize the .aspx files and the Application.Master file as needed.

 

Method 2: Create a custom Layouts folder
Note This method will change the layouts directory for any site collection within the Web application that is being modified. To apply custom layouts changes to an individual site collection, the site collection should reside in its own Web application.

1.
Create a custom LayoutsSiteCollection folder to contain a copy of the originally installed files and folders. For example, create a LayoutsSiteCollection folder in the following location:

C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Layouts\LayoutsSiteCollection

Note The SiteCollection placeholder is the name of a site collection.

2.
Copy the originally installed files and folders from the Layouts folder to the LayoutsSiteCollection folder that you created in step 1. For example, copy the originally installed files and folders from the following folder to the LayoutsSiteCollection folder:

C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\Template\Layouts

3.
Start Internet Information Services (IIS) Manager. To do this, click Start, point to All Programs, point to Administrative Tools, and then click Internet Information Services (IIS) Manager.

4.
In IIS Manager, follow these steps:

a.
Expand the Web site that is hosting the site collection.

b.
Right-click _layouts, and then click Properties.

c.
Click the Virtual Directory tab.

d.
Click Browse, change the path from the Layouts folder to the LayoutsSiteCollection folder, and then click OK two times.

5.
In the LayoutsSiteCollection folder, customize the .aspx files and the Application.Master file as needed.

6.
Repeat these steps for each site collection that you have to customize.

Advantage of Method 2


This method enables the customization of application pages for individual site collections.

Limitations of Method 2


If a public update, a hotfix package, or a service pack is installed that contains updates to the files in the Layouts folder, the update is not applied to your custom Layouts folder.


This method may cause excessive manageability and maintenance issues.


Any hard-coded functionality in SharePoint Server 2007 or Windows SharePoint Services 3.0 that references the Layouts folder instead of the _layouts virtual directory may not function as expected.

 


APPLIES TO


Microsoft Office SharePoint Server 2007


Microsoft Windows SharePoint Services 3.0

 

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http://support.microsoft.com/kb/944105