Eclipse 3.0 introduced a new run-time system based on OSGi standards that uses bundles and a new manifest file (MANIFEST.MF) to implement plug-ins. The use of MANIFEST.MF, in normal circumstances, is completely optional.
You will notice that almost all of the 3.0 SDK plug-ins do NOT have one yet all are marked as 3.0 and many do not require the compatibility layer. The only reason you would want to have a MANIFEST.MF is if you need to use a particular OSGi capability that is not exposed through plugin.xml (for example, import-package).
Otherwise it's recommended at this time that you don't have one.