You can create a config file like the one used before Basic4ppc v6. This file forces your application to run with a specific version of the .Net Framework.
You should create a file named YourApp.exe.config with the following content:
<configuration>
<startup>
<supportedRuntime version="v3.5.7283"/>
<supportedRuntime version="v2.0.7045"/>
<supportedRuntime version="v2.0.6129"/>
<supportedRuntime version="v2.0.5238"/>
</startup>
</configuration>
Remove or add versions that you want to support. I'm not sure if the first one is the latest version of .Net CF 3.5.
This file should be distributed together with your application.