OK, after reading and understanding this a bit better, I got it working. I removed the DirectoryCatalog from the AggregateCatalog, and added the .dlls in the Plugins-folder to AssemblySource.Instance before creating the AggregateCatalog.
This way it worked for both Caliburn.Micro and MEF.
New bootstrapper code:
protected override void Configure()
{
string pluginPath = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "Plugins");
if (!Directory.Exists(pluginPath))
Directory.CreateDirectory(pluginPath);
var fi = new DirectoryInfo(pluginPath).GetFiles("*.dll");
AssemblySource.Instance.AddRange(fi.Select(fileInfo => Assembly.LoadFrom(fileInfo.FullName)));
var catalog = new AggregateCatalog(
AssemblySource.Instance.Select(x => new AssemblyCatalog(x)).OfType<ComposablePartCatalog>()
);
_container = new CompositionContainer(catalog);
var batch = new CompositionBatch();
batch.AddExportedValue<IWindowManager>(new WindowManager());
batch.AddExportedValue<IEventAggregator>(new EventAggregator());
batch.AddExportedValue(_container);
_container.Compose(batch);
}