WSS with SP2 can run in 32-bit emulation mode on a 64-bit machine/OS but there are a few manual steps that need to be done in order to get that working.

Step 1 - First of all, set the IIS application pool to run as 32 bit. On 64 bit machines, SharePoint runs in 32-bit emulation mode. This means that you need to update IIS settings so that the IIS application pool processes run as 32 bit processes. One caveat here is that the setting that controls this applies to all application pool processes. This means that all IIS app pools will run either as 32 bit or as 64 bit but not both. To do that you will have to set the W3SVC/AppPools/Enable32bitAppOnWin64 metabase property to 1. For more details see KB article http://support.microsoft.com/default.aspx?scid=kb;en-us;895976

To do that run the following commands from the command prompt
    CScript "%SystemDrive%\InetPub\AdminScripts\adsutil.vbs" set w3svc/AppPools/Enable32bitAppOnWin64 1
    iisreset

Step 2 - Enable the ASP.NET extensions for the 32 bit ASP.NET version. To do that you will have to run the commands below from the "Visual Studio 2005 Command Prompt".
    %SystemRoot%\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis -i -enable
    iisreset

Make sure you run this command from the Framework folder and not from the Framework64 folder.

Step 3 - Install the slipstream version of WSS 2003 with SP2 (kit of WSS 2003 containing SP2 instead of kit of WSS 2003 and then separately apply SP2). If you don't install the slipstream version of WSS 2003 with SP2, then I think you need to first install .Net Framework 1.1 as described by step 2 in http://support.microsoft.com/Default.aspx?id=905854.


Troubleshooting and fixing errors
I purposely reproed a few of the errors that I knew you could run into in order to see how these errors manifest themselves and how they can be fixed.

A) Windows SharePoint Services requires a more recent version of Microsoft ASP.Net. To install a more recent version, go to Add or Remove Programs, click Add/Remove Windows Components, click Application Server, click Details, and then select ASP.NET.

This error is raised by Windows SharePoint Services 2003 with SP1 setup when the .Net Framework 1.1 is not installed. This error is also raised when you have installed .Net Framework but it's version 2.0. This error is not raised by Windows SharePoint Services 2003 with SP2 setup. Windows SharePoint Services 2003 with SP2 supports .Net Framework 2.0 and you are going to need it anyway if you want to run WSS on the 64 bit OS. So instead of installing WSS 2003 with SP1, you should download and install WSS 2003 with SP2 from here http://www.microsoft.com/downloads/details.aspx?familyid=B922B28D-806A-427B-A4C5-AB0F1AA0F7F9&displaylang=en.

The .Net Framework installation instructions from the error message do not apply to the 64 bit OS, so you will have to download and install the .Net Framework 2.0 from one of these 2 links
Microsoft .NET Framework Version 2.0 Redistributable Package (x64) - http://www.microsoft.com/downloads/details.aspx?familyid=B44A0000-ACF8-4FA1-AFFB-40E78D788B00&displaylang=en
Microsoft .NET Framework Version 2.0 Redistributable Package (IA64) - http://www.microsoft.com/downloads/details.aspx?familyid=53C2548B-BEC7-4AB4-8CBE-33E07CFC83A7&displaylang=en

B) Windows SharePoint Services requires a more recent version of Microsoft ASP.NET. Go to the Microsoft Web site at www.microsoft.com to download and install a more recent version.
This error is raised by Windows SharePoint Services with SP2 when one of the following is true
       1 - .Net Framework has not been installed on the machine. See bulet A) above on how to download and install .Net Framework.
       2 - .Net Framework has been installed but ASP.NET is not enabled. See step 2 above on how to enable ASP.NET
       3 - ASP.NET has been installed, but IIS application pools are running in 64 bit mode. See step 1 above on how to switch the app pools to 32 bit mode.

C) The Microsoft .Net Framework version 1.1.4322 must be installed before this package can be installed.
WSS 2003 with SP2 does not require .Net Framework 1.1 if 2.0 is installed but somehow I managed to get the machine in this state and after that I couldn't remove or re-install SharePoint. No matter what I did, I got the same error message referring to .Net Framework 1.1.
If your machine is in this state you can remove SharePoint by temporarilly installing .Net Framework 1.1 from here http://www.microsoft.com/downloads/details.aspx?FamilyId=262D25E3-F589-4842-8157-034D1E7CF3A3&displaylang=en.
Then you can re-install and configure WSS 2003 with SP2 and only after that remove .Net Framework 1.1.

D) RpcProxy.dll failed to load
If you get the following 2 errors in the Application Event Log, then you need to uninstall/reinstall RPC Over HTTP Proxy. You will have to do that from Control Panel -> Add Remove Programs -> Add/Remove Windows Components -> Networking Services -> RPC Over HTTP Proxy

Event Type: Error
Event Source: W3SVC-WP
Event Category: None
Event ID: 2214
Date:  11/16/2005
Time:  12:58:23 PM
User:  N/A
Computer: MachineName
Description:
The HTTP Filter DLL C:\WINDOWS\System32\RpcProxy\RpcProxy.dll failed to load.  The data is the error.

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
Data:
0000: 7e 00 00 00               ~...   

Event Type: Error
Event Source: W3SVC-WP
Event Category: None
Event ID: 2214
Date:  11/16/2005
Time:  12:58:23 PM
User:  N/A
Computer: MachineName
Description:
The HTTP Filter DLL C:\WINDOWS\System32\RpcProxy\RpcProxy.dll failed to load.  The data is the error.

For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
Data:
0000: 7e 00 00 00               ~...   

E) Could not load all ISAPI filters for site/service. Therefore startup aborted.
or
ISAPI Filter 'path to filter' could not be loaded due to a configuration problem. The current configuration only supports loading images built for a AMD64 processor architecture. The data field contains the error number. To learn more about this issue, including how to troubleshooting this kind of processor architecture mismatch error, see http://go.microsoft.com/fwlink/?LinkId=29349.

You probably
    1 - skipped step 1)
    2 - you performed step 1) but then some other application has reverted the setting so that the IIS app pools run as 64 bit
    3 - you have 32 bit and 64 bit filters installed on the same machine in which case only one set of the filters will work

Installing SharePoint Portal Server 2003 SP2 on a Windows Server 2003 x64 Edition
For installing SharePoint Portal Server 2003 SP2 on a Windows Server 2003 x64 Edition see the following KB article http://support.microsoft.com/Default.aspx?id=905854