I want to be able to upgrade from 2003 to 2008 without any loss of files or programs.
Is this possible to do?
Yes, if the two systems use the same language and the same CPU architecture (x86 or x64).
But be careful, because maybe some hardware and/or applications you have on the server don't work on Windows Server 2008; be sure to check for compatibility issues.
Also, although in-place upgrades of the O.S. are supported, they're usually not considered best practice because they lead to an "unclean" installation.
These three articles discuss how to upgrade from Windows Server 2003 to Windows Server 2008. These all come from the Microsoft Support website.
Good luck on your upgrades!
I wouldn't personally do this as an in-place upgrade. There are a lot of differences between Server 2003 & Server 2008, and chances are you will find things not working after the upgrade. However, if you really can't avoid a clean install, you should at least do a test upgrade on a separate machine or VM.
You can if you are upgrading to the same architecture, as already mentioned.
If you are running Server 2003 x86 you might want to just do a clean install of x64 2008 or R2. Microsoft will not be releasing any more x86 server operating systems, so you can expect x86 application support to start to decline as well as not having an upgrade path past 2008. 2008 R2, for example, is x64 only.