One of the transparent benefits of building your projects with VS2005 is that the default File Alignment is now set at 512 bytes, rather than the 4096 bytes which was the default for device projects in VS2003. This means if you create a new project in both versions and add exactly the same code you should notice the output dll created by VS2005 is noticably smaller.
One thing you may not realise is that the default value used in a VS2003 project is stored within the C# project file, which means if you import a VS2003 C# Smart Device project to VS2005 it will still use the value 4096. You can change this from the project properties > Build tab > Advanced button and set it to 512.