Note: Advice in this article will only work for JxBrowser 6. See the corresponding article for JxBrowser 7 here and here.

To get information about all installed and available plugins you can use the PluginManager.getPluginsInfo() method:
PluginManager pluginManager = browser.getPluginManager();
List<PluginInfo> pluginsList = pluginManager.getPluginsInfo();
for (PluginInfo plugin : pluginsList) {
    System.out.println("Plugin Name: " + plugin.getName());

To enable/disable specified plugin register your own PluginFilter implementation:

pluginManager.setPluginFilter(new PluginFilter() {
    public boolean isPluginAllowed(PluginInfo pluginInfo) {
        // Allow only PDF plugin
        return pluginInfo.getMimeTypes().contains("application/pdf");