The IApplication is part of Equinox, and uses the registry to find out what is installed. So as well as including the appropriate jars in PAX, you'll also need to ensure that you start at least declarative services and the extension registry bundles, as otherwise the IApplication stuff won't be found.
Secondly there is no bundle that calls the EclipseStarter class, which is the thing that handles the main arguments, and which passes that through to the runtime. So unless you're doing that yourself, you will find that the application won't run at all.
If you're starting Eclipse specifically you might find some Eclipse-specific arguments to specify these as Java system properties:
http://help.eclipse.org/luna/index.jsp?topic=%2Forg.eclipse.platform.doc.isv%2Freference%2Fmisc%2Fruntime-options.html
for example, you could specify -Dapplication.id=yourapp
You might also try eclipse.commands as a newline-separated list of arguments.